<PAGE>

                                                                    Exhibit 4.29

                   JUNIOR SUBORDINATED DEBENTURE CERTIFICATE

     THE SECURITIES WILL BE ISSUED AND MAY BE TRANSFERRED ONLY IN BLOCKS HAVING
AN AGGREGATE PRINCIPAL AMOUNT OF NOT LESS THAN $100,000. ANY ATTEMPTED TRANSFER
OF SECURITIES IN A BLOCK HAVING AN AGGREGATE PRINCIPAL AMOUNT OF LESS THAN
$100,000 AND MULTIPLES OF $1,000 IN EXCESS THEREOF SHALL BE DEEMED TO BE VOID
AND OF NO LEGAL EFFECT WHATSOEVER. ANY SUCH PURPORTED TRANSFEREE SHALL BE DEEMED
NOT TO BE THE HOLDER OF SUCH SECURITIES FOR ANY PURPOSE, INCLUDING, BUT NOT
LIMITED TO, THE RECEIPT OF PRINCIPAL OF OR INTEREST ON SUCH SECURITIES, AND SUCH
PURPORTED TRANSFEREE SHALL BE DEEMED TO HAVE NO INTEREST WHATSOEVER IN SUCH
SECURITIES.
<PAGE>

                              GREATER BAY BANCORP

CUSIP No.:  391648-AF9
            $41,000,000

      10.75%  JUNIOR SUBORDINATED DEFERRABLE INTEREST DEBENTURE

                           DUE June 1, 2030 Series B

     Greater Bay Bancorp, a California corporation (the "Corporation," which
term includes any successor Person under the Indenture hereinafter referred to),
for value received, hereby promises to pay to GBB Capital IV or registered
assigns, the principal sum of Forty-One Million Dollars ($41,000,000) on June 1,
2030 (the "Maturity Date"), unless previously prepaid, and to pay interest on
the outstanding principal amount hereof from May 19, 2000, or from the most
recent interest payment date (each such date, an "Interest Payment Date") to
which interest has been paid or duly provided for, semi-annually (subject to
deferral as set forth herein) in arrears on June 1st and December 1st of each
year, commencing December 1, 2000 at the rate of 10.75% per annum, until the
principal hereof shall have become due and payable, and on any overdue principal
and premium, if any, and (without duplication and to the extent that payment of
such interest is enforceable under applicable law) on any overdue installment of
interest at the same rate per annum compounded semi-annually ("Compounded
Interest"). The amount of interest payable hereon shall be computed on the basis
of a 360-day year of twelve 30-day months. In the event that any date on which
the principal of (or premium, if any) or interest on this Security is payable is
not a Business Day (as defined in the Indenture), then the payment payable on
such date will be made on the next succeeding day that is a Business Day (and
without any interest or other payment in respect of any such delay), with the
same force and effect as if made on such date. Pursuant to the Indenture, in
certain circumstances the Corporation will be required to pay Additional Sums
(as defined in the Indenture) with respect to this Security. Pursuant to the
Registration Rights Agreement and the Liquidated Damages Agreement, in certain
limited circumstances the Corporation will be required to pay Liquidated Damages
(as defined in the Registration Rights Agreement and the Liquidated Damages
Agreement) with respect to this Security.

     The interest installment so payable, and punctually paid or duly provided
for, on any Interest Payment Date will, as provided in the Indenture, be paid to
the Person in whose name this Security (or one or more Predecessor Securities,
as defined in said Indenture) is registered at the close of business on the
regular record date for such interest installment, which shall be at the close
of business on the 15th day of the month immediately preceding the month in
which the relevant Interest Payment Date falls. Any such interest installment
not punctually paid or duly provided for shall forthwith cease to be payable to
the holders on such regular record date and may be paid to the Person in whose
name this Security (or one or more Predecessor Securities) is registered at the
close of business on a special record date to be fixed by the Debenture Trustee
for the payment of such defaulted interest, notice whereof shall be given to the
holders of Securities not less than 10 days prior to such special record date,
or may be paid at any time in any other lawful manner not inconsistent with the
requirements of any securities exchange on
<PAGE>

which the Securities may be listed, and upon such notice as may be required by
such exchange, all as more fully provided in the Indenture.

     The principal of and interest (including Compounded Interest and Additional
Sums, if any) and Liquidated Damages, if any, on this Security shall be payable
at the office or agency of the Debenture Trustee maintained for that purpose in
any coin or currency of the United States of America that at the time of payment
is legal tender for payment of public and private debts; provided, however, that
                                                         --------  -------
payment of interest may be made at the option of the Corporation by (i) check
mailed to the holder at such address as shall appear in the Security Register or
(ii) transfer to an account maintained by the Person entitled thereto, provided
that proper written transfer instructions have been received by the relevant
record date.  Notwithstanding the foregoing, so long as the holder of this
Security is the Property Trustee of GBB Capital IV, the payment of the principal
of and interest (including Compounded Interest and Additional Sums, if any) and
Liquidated Damages, if any, on this Security will be made at such place and to
such account as may be designated by such Property Trustee.

     The indebtedness evidenced by this Security is, to the extent provided in
the Indenture, subordinate and junior in right of payment to the prior payment
in full of all Senior Indebtedness, and this Security is issued subject to the
provisions of the Indenture with respect thereto.  Each holder of this Security,
by accepting the same, (a) agrees to and shall be bound by such provisions, (b)
authorizes and directs the Debenture Trustee on his or her behalf to take such
action as may be necessary or appropriate to acknowledge or effectuate the
subordination so provided and (c) appoints the Debenture Trustee his or her
attorney-in-fact for any and all such purposes.  Each holder hereof, by his or
her acceptance hereof, hereby waives all notice of the acceptance of the
subordination provisions contained herein and in the Indenture by each holder of
Senior Indebtedness, whether now outstanding or hereafter incurred, and waives
reliance by each such holder upon said provisions.

     This Security shall not be entitled to any benefit under the Indenture or
be valid or become obligatory for any purpose until the Certificate of
Authentication hereon shall have been signed by or on behalf of the Debenture
Trustee.

     The provisions of this Security are continued on the reverse side hereof
and such provisions shall for all purposes have the same effect as though fully
set forth at this place.

                                       3
<PAGE>

     IN WITNESS WHEREOF, the Corporation has caused this instrument to be duly
executed and sealed this 20/th/ day of November, 2000.

                              GREATER BAY BANCORP


                              By: /s/ Shawn E. Saunders
                                  ---------------------
                                  Shawn E. Saunders
                                  Senior Vice President, Finance
                                  and Accounting



Attest:


By: /s/ Linda M. Iannone
    --------------------
    Linda M. Iannone
    Senior Vice President, General
    Counsel and Secretary

                                       4
<PAGE>

                         CERTIFICATE OF AUTHENTICATION

     This is one of the 10.75% Junior Subordinated Deferrable Interest
Debentures, Series B, of GREATER BAY BANCORP referred to in the within-mentioned
Indenture.

                               WILMINGTON TRUST COMPANY,
                               not in its individual capacity but solely as
                               Debenture Trustee



Dated:  November 20, 2000      By: /s/ Bruce L. Bisson
                                   -------------------
                               Authorized Signatory

                                       5
<PAGE>

     This Security is one of the Securities of the Corporation (herein sometimes
referred to as the "Securities"), specified in the Indenture, all issued or to
be issued under and pursuant to an Indenture, dated as of May 19, 2000 (the
"Indenture"), duly executed and delivered between the Corporation and Wilmington
Trust Company, as Debenture Trustee (the "Debenture Trustee"), to which
Indenture reference is hereby made for a description of the rights, limitations
of rights, obligations, duties and immunities thereunder of the Debenture
Trustee, the Corporation and the holders of the Securities. The Securities are
limited in aggregate principal amount as specified in the Indenture.

     Upon the occurrence and continuation of a Special Event (as defined in the
Indenture) prior to June 1, 2010 (the "Initial Optional Redemption Date"), the
Corporation shall have the right, at any time within 90 days following the
occurrence of such Special Event, to prepay this Security in whole (but not in
part) at the Special Event Prepayment Price. "Special Event Prepayment Price"
shall mean, with respect to any prepayment of the Securities following a Special
Event, an amount in cash equal to 100% of the principal amount of the Securities
to be prepaid, plus any accrued and unpaid interest (including Compounded
Interest and Additional Sums, if any) and Liquidated Damages, if any, thereon to
the date of such prepayment.

     In addition, the Corporation shall have the right to prepay this Security,
in whole or in part, at any time on or after the Initial Optional Redemption
Date (an "Optional Prepayment"), at 100% of the principal amount of this
Security plus, in each case, accrued and unpaid interest thereon (including
Compounded Interest and Additional Sums, if any) and Liquidated Damages, if any,
thereon to the applicable date of prepayment (the "Optional Prepayment Price").

     The Prepayment Price shall be paid prior to 12:00 noon, New York City time,
on the date of such prepayment or at such earlier time as the Corporation
determines, provided that the Corporation shall deposit with the Debenture
            --------
Trustee an amount sufficient to pay the Prepayment Price by 10:00 a.m., New York
City time, on the date such Prepayment Price is to be paid.  Any prepayment
pursuant to this paragraph will be made upon not less than 30 days nor more than
60 days' prior written notice.

     If the Securities are only partially prepaid by the Corporation pursuant to
an Optional Prepayment, the particular Securities to be prepaid shall be
selected on a pro rata basis from the outstanding Securities not previously
called for prepayment; provided, however, that with respect to Securityholders
                       --------  -------
that would be required to hold Securities with an aggregate principal amount of
less than $100,000 but more than an aggregate principal amount of zero as a
result of such pro rata prepayment, the Corporation shall prepay Securities of
each such Securityholder so that after such prepayment such Securityholder shall
hold Securities either with an aggregate principal amount of at least $100,000
or such Securityholder no longer holds any Securities and shall use such method
(including, without limitation, by lot) as the Corporation shall deem fair and
appropriate; provided, further, that any such proration may be made on the basis
             --------  -------
of the aggregate principal amount of Securities held by each Securityholder
thereof and may be made by making such adjustments as the Corporation deems fair
and appropriate in order that only Securities in denominations of $1,000 or
integral multiples thereof shall be prepaid.  In the event of prepayment of this
Security in part only, a new Security or Securities for the portion hereof that
has not been prepaid will be issued in the name of the holder hereof upon the
cancellation hereof.

                                       6
<PAGE>

     Notwithstanding the foregoing, any prepayment of Securities by the
Corporation shall be subject to the receipt of any and all required regulatory
approvals.

     In case an Event of Default (as defined in the Indenture) shall have
occurred and be continuing, the principal of all of the Securities may be
declared, and upon such declaration shall become, due and payable, in the
manner, with the effect and subject to the conditions provided in the Indenture.

     The Indenture contains provisions permitting the Corporation and the
Debenture Trustee, with the consent of the holders of a majority in aggregate
principal amount of the Securities at the time outstanding (as defined in the
Indenture), to execute supplemental indentures for the purpose of adding any
provisions to or changing in any manner or eliminating any of the provisions of
the Indenture or of modifying in any manner the rights of the holders of the
Securities; provided, however, that no such supplemental indenture shall,
            --------  -------
without the consent of each holder of Securities then outstanding and affected
thereby, (i) change the Maturity Date of any Security, or reduce the rate or
extend the time of payment of interest thereon (subject to Article XVI of the
Indenture), or reduce the principal amount thereof, or change any of the
prepayment provisions or make the principal thereof or any interest or premium
thereon payable in any coin or currency other than U.S. dollars, or impair or
affect the right of any holder of Securities to institute suit for payment
thereof, or (ii) reduce the aforesaid percentage of Securities the holders of
which are required to consent to any such supplemental indenture.  The Indenture
also contains provisions permitting the holders of a majority in aggregate
principal amount of the Securities at the time outstanding affected thereby, on
behalf of all of the holders of the Securities, to waive any past default in the
performance of any of the covenants contained in the Indenture, or established
pursuant to the Indenture, and its consequences, except a default in the payment
of the principal of or premium, if any, or interest on any of the Securities or
a default in respect of any covenant or provision under which the Indenture
cannot be modified or amended without the consent of each holder of Securities
then outstanding.  Any such consent or waiver by the holder of this Security
(unless revoked as provided in the Indenture) shall be conclusive and binding
upon such holder and upon all future holders and owners of this Security and of
any Security issued in exchange herefor or in place hereof (whether by
registration of transfer or otherwise), irrespective of whether or not any
notation of such consent or waiver is made upon this Security.

     No reference herein to the Indenture and no provision of this Security or
of the Indenture shall alter or impair the obligation of the Corporation, which
is absolute and unconditional, to pay the principal of (and premium, if any) and
interest (including Compounded Interest and Additional Sums, if any) and
Liquidated Damages, if any, on this Security at the time and place and at the
rate and in the money herein prescribed.

     So long as no Event of Default shall have occurred and be continuing, the
Corporation shall have the right, at any time and from time to time during the
term of the Securities, to defer payments of interest by extending the interest
payment period (an "Extended Interest Payment Period") of such Securities for a
period not (i) exceeding 10 consecutive semi-annual periods, including the first
such semi-annual period during such extension period, (ii) extending beyond the
Maturity Date of the Securities or (iii) ending on a date other than an Interest
Payment Date, at the end of which period the Corporation shall pay all interest
then accrued and unpaid

                                       7
<PAGE>

(together with interest thereon at the rate specified for the Securities to the
extent that payment of such interest is enforceable under applicable law).
Before the termination of any such Extended Interest Payment Period, the
Corporation may further defer payments of interest by further extending such
Extended Interest Payment Period, provided that such Extended Interest Payment
Period, together with all such previous and further extensions within such
Extended Interest Payment Period, (i) shall not exceed 10 consecutive semi-
annual periods including the first semi-annual period during such Extended
Interest Payment Period, (ii) shall not end on any date other than an Interest
Payment Date, and (iii) shall not extend beyond the Maturity Date of the
Securities. Upon the termination of any such Extended Interest Payment Period
and the payment of all accrued and unpaid interest and any additional amounts
then due, the Corporation may commence a new Extended Interest Payment Period,
subject to the foregoing requirements. No interest shall be due and payable
during an Extended Interest Payment Period, except at the end thereof, but the
Corporation may prepay at any time all or any portion of the interest accrued
during an Extended Interest Payment Period.

     The Corporation has agreed that it will not (i) declare or pay any
dividends or distributions on, or redeem, purchase, acquire, or make a
liquidation payment with respect to, any of the Corporation's capital stock,
(ii) make any payment of principal of or premium, if any, or interest on or
repay, repurchase or redeem any debt securities of the Corporation (including
Other Debentures) that rank pari passu with or junior in right of payment to the
Securities or (iii) make any guarantee payments with respect to any guarantee by
the Corporation of the debt securities of any Subsidiary of the Corporation
(including Other Guarantees) if such guarantee ranks pari passu with or junior
in right of payment to the Securities (other than (a) dividends or distributions
in shares of, or options, warrants or rights to subscribe for or purchase shares
of, Common Stock), (b) any declaration of a dividend in connection with the
implementation of a stockholders' rights plan, or the issuance of stock under
any such plan in the future, or the redemption or repurchase of any such rights
pursuant thereto, (c) payments under the Capital Securities Guarantee, as
defined in the Indenture, (d) as a result of a reclassification of the
Corporation's capital stock or the exchange or conversion of one class or series
of the Corporation's capital stock for another class or series of the
Corporation's capital stock, (e) the purchase of fractional interests in shares
of the Corporation's capital stock pursuant to the conversion or exchange
provisions of such capital stock or the security being converted or exchanged
and (f) purchases of Common Stock related to the issuance of Common Stock or
rights under any of the Corporation's benefit or compensation plans for its
directors, officers or employees or any of the Corporation's dividend
reinvestment plans), if at such time (1) there shall have occurred any event of
which the Corporation has actual knowledge that (a) is a Default or an Event of
Default and (b) in respect of which the Corporation shall not have taken
reasonable steps to cure, (2) such Securities are held by the Property Trustee
of GBB Capital IV and the Corporation shall be in default with respect to its
payment of any obligations under the Capital Securities Guarantee or (3) the
Corporation shall have given notice of its election to exercise its right to
commence an Extended Interest Payment Period and shall not have rescinded such
notice, and such Extended Interest Payment Period or any extension thereof shall
have commenced and be continuing.

     Subject to (i) the Corporation having received any required regulatory
approvals and (ii) the Administrative Trustees of GBB Capital IV having received
an opinion of counsel to the effect that such distribution will not cause the
holders of Capital Securities to recognize gain or

                                       8
<PAGE>

loss for federal income tax purposes, the Corporation will have the right at any
time to liquidate the Trust and, after satisfaction of liabilities of creditors
of the Trust as required by applicable law, to cause the Securities to be
distributed to the holders of the Trust Securities in liquidation of the Trust.

     The Securities are issuable only in registered form without coupons in
minimum denominations of $100,000 and multiples of $1,000 in excess thereof.  As
provided in the Indenture and subject to the transfer restrictions limitations
as may be contained herein and therein from time to time, this Security is
transferable by the holder hereof on the Security Register of the Corporation,
upon surrender of this Security for registration of transfer at the office or
agency of the Corporation in Wilmington, Delaware accompanied by a written
instrument or instruments of transfer in form satisfactory to the Corporation or
the Debenture Trustee duly executed by the holder hereof or his or her attorney
duly authorized in writing, and thereupon one or more new Securities of
authorized denominations and for the same aggregate principal amount will be
issued to the designated transferee or transferees.  No service charge will be
made for any such registration of transfer, but the Corporation may require
payment of a sum sufficient to cover any tax or other governmental charge
payable in relation thereto.

     Prior to due presentment for registration of transfer of this Security, the
Corporation, the Debenture Trustee, any authenticating agent, any paying agent,
any transfer agent and the security registrar may deem and treat the holder
hereof as the absolute owner hereof (whether or not this Security shall be
overdue and notwithstanding any notice of ownership or writing hereon made by
anyone other than the security registrar for the Securities) for the purpose of
receiving payment of or on account of the principal hereof and premium, if any,
and (subject to the Indenture) interest due hereon and for all other purposes,
and neither the Corporation nor the Debenture Trustee nor any authenticating
agent nor any paying agent nor any transfer agent nor any security registrar
shall be affected by any notice to the contrary.

     No recourse shall be had for the payment of the principal of or premium, if
any, or interest (including Compounded Interest and Additional Sums, if any) or
Liquidated Damages, if any, on this Security, or for any claim based hereon, or
otherwise in respect hereof, or based on or in respect of the Indenture, against
any incorporator, stockholder, employee, officer or director, past, present or
future, as such, of the Corporation or of any predecessor or successor Person,
whether by virtue of any constitution, statute or rule of law, or by the
enforcement of any assessment or penalty or otherwise, all such liability being,
by the acceptance hereof and as part of the consideration for the issuance
hereof, expressly waived and released.

     All terms used in this Security that are defined in the Indenture shall
have the meanings assigned to them in the Indenture.

     THE INDENTURE AND THE SECURITIES SHALL BE GOVERNED BY AND CONSTRUED IN
ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO CONFLICT OF
LAW PRINCIPLES THEREOF.



                                       9