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1

Protein Data Bank
https://pdb.org• PDB: 1st Open Access digital
resource in biology(est. in 1971 with 7 entries)

Nature New Biology 233, page 223 (1971)• Initially, managed jointly by data
centers in US and UK• Today, single global
PDB macromolecular structurearchive(>198,000 entries)2

生体高分子の3次元構造（形）に関する情報を集めた国際的データベース
1971年からのデータが集積され，情報は無償で利用できる．
運営は各国（米国，欧州，日本）の政府機関による研究費用でまかなわれている．2003年からは国際組織wwPDBとして活動している（PDBjは創立メンバー）．

After solving structure, what we should do?

https://wwpdb.org

PDBj is in charge of processing and annotating
the data from Asian and Middle-east regions．

Nature New Biology 233, page 223 (1971)200000

Science 245, 1179-1181 (1989)

180000~~~~N NWl

160000140000The Missing Crystallography Data

120000Some disgruntled researchers are mounting a campaign to force crystallographers to make available
key data when they publish the structure of complex molecules

•

2016

2014

2012

•

2000
2004 2002

IUCr published a formal guideline for data depsition.

Downloaded from https://www.science.org at Osaka University on October 22, 2021

2020

2018

2006
2010 2008

100000SHOULD A SCIENTISr be allowed to publish the primary results on which the condusions prove their accuracy or to reap scientificonly the conclusions of a piece of research were based-the three-dimensional coordi- rewards after the years invested in obtaining
while keeping secret the data and results on nates describing the position of every atom them. And, in the case of structure laborawhich those conclusions are based? That's in the molecule under study. Without those tories springing up in many drug compa80000
what some say is happening in the field of x- coordinates a structure article is nearly use- nies, there can be a strong incentive to keep
ray crystallography, where an increasingly less to many researchers who may want to information secret in order to cash in on its
vocal group of disgruntled researchers are verify or build on the work.
commercial value.
60000
accusing colleagues of sitting on vital inforIn an effort to change the system, 2 years
While the urge to withhold vital informamation and thus slowing the progress of ago Yale crystallographer Frederic Richards tion can tempt a researcher in any field, thescience.
began a crusade to get journals to force nature of crystallography provides a conve"Publication means making public," says authors to make their primary data public. nient excuse for not sharing. The raw x-ray
40000
crystallographer Richard Dickerson of the He was joined by 173 colleagues, who co- diffraction data generated during structure
University of California, Los Angeles. "I signed a letter imploring journals to take a studies of proteins and nucleic acids, and the
don't know of any other field of science stand. And indeed, some have changed their atomic coordinates derived from them, conwhere you are required to make public policies, now requiring crystallographers to sist of tables of numbers too voluminous to20000
neither your data nor your results, only your make coordinates available within a reason- fit easily into a journal article. So researcherscommentaries."
able amount of time following publication have traditionally left them out.
Biochemist Howard Schachman, at the of their papers. But some researchers are still
National
LaboBrookhaven
Since 1971,
University of California, Berkeley, gripes: not doing so, prompting Dickerson 2 ratory has maintained a data bank for stor0"[People] publish, they get the scientific months ago to fire off a "dear colleague" age and distribution of x-ray data and coorprestige, and then they don't make the real letter in which he warned his colleagues that dinates. But researchers deposit their data in 1976
results available, which are needed to assess "we are on our way to developing a minia- the bank on an entirely voluntary basis,
and1978
the validity of the work, and allow people to ture scandal."The data bank curmany do not volunteer.1980
extend it."That's not how every crystallographer sees 1984
435 sets of coordinates available,
rently has 1982
What has scientists like Schachman and it. Although few will publicly1986
advocate many of which are multiple sets for the same
1988
Dickerson upset is that journals allow x-ray withholding coordinates
indefinitely, many macromolecule. But data bank directorof argue 1990
crystallographers to publish the structures1992
that there are valid reasons not to Thomas Koetzle says there are more than 70
macromolecules without making
1994available release them immediately-to further im- molecules for which structures have been
published but no coordinates deposited. In
1998 1996
Growing gap. Crystallographer Richard Dick- some cases, years have gone by since publierson (below) found that coordinates have been cation.
UCLA's Dickerson has found what is todeposited for less than half the published DNAstructures (left). "That really is pretty sickening," him particularly depressing evidence of this.
he says.
While writing a review on DNA structure
recently, he discovered that, of the 78 DNA
structures published, the coordinates for
only 29 had been deposited at Brookhaven(see figure). Some of the structures withoutstcoordinates were nearly a decade old. "Thatreally is pretty sickening," says Dickerson.
To Yale's Richards, journal editors are thekey. "If the journals took a stand, then [thewithholders] would be stuck," he says. "Ifthey're going to publish, they have to follow
the rules, and if they don't want to follow
the rules, they don't publish."
But Richards' effort to persuade journals
to establish rules has drawn a mixed response. Of about 40 journals he contacted,
he says eight, including theJournal ofBiological Chemistry UBC), Biochemistry, and Science,
have changed their policies, and at least
seven more, including the Proceedings of the

Number of Entire Entries
Number of Yearly Depositions

Structure Factors became mandatory for PDB depsition from Feb 1 2008.

Science 317, 194-195 (2007)

NEWS & COMMENT 1179

How to know the 3D structure?
M TG CAW G AP TF
QE
G CFN・・・

https://pdbj.org

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PDBで提供するFileFormat●mmCIFThe canonical format of the wwPDB.
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実験データ• Validation Report (PDF, XML, RDF)

検証レポート8

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今⽉の分⼦（⽉替わりの分⼦構造紹介記事）

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・統計ページ・PDB検索（PDBj Mine2)
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・MolmilPDB IDがわかっている構造を⾒たい！
[CASE #1] Keyword searchusing PDB ID

5ZF0 ⏎PDB IDs are written in thestructure paper or related review.

②②①③[CASE #1] Keyword searchusing PDB ID from the article
Summary page of the entry “5ZF0”
will be shown. You can go to the①linked other databases,②download the coordinates,and ③take a look at thestructure of biological unit using
the standard web browser on youPC.

P0A3C9[CASE #2] Keyword searchusing SEQ ID

P0A3C9 ⏎興味のあるタンパク質の構造を調べたい！

List of the entries containing“P0A3C9” will be shown. You canselect the entry with the highest
resolution.

1. Select moleculeSummary page of the entry“5AUI” includes

1. PDB ID
2. Entry Name
3. Viewer
4. Reference
5. Link to other DB
6. Validation実際にやってみます・統計ページ・PDB検索（PDBj Mine2)
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・MolmilJournal

PDB Entries as a
Primary Citation

PDB Entries with
Any Citations

OldestDeposition toPDB

HighestResolution in theJournal

J. Bichem.

317457

1st August, 1976

0.90 Å

J. Biol. Chem.

12,94515,031

1st April, 1975

0.80 Å

Biochem.

10,747

12,552

1st March, 1975

0.78 Å

FEBS J.

1,688

2,156

11th June, 1985

0.95 Å

FEBS Lett.

834

1,395

9th June, 1986

1.00 Å

14%

Oxidoreductases
18%

3%

Transferases
12%

6%
Others
39%

77%

Enzyme61%

Hydrolases
23%
Lyases3%
Isomerases
2%~ 10K

10K ~ 50K

50K ~100K

100K ~

Ligases
3%
Translocases
0%2,5001000

Number of entries

50

J. Biochem.

4.8
4.6 -4.8

Resolution [Å]

2,500

2,000

2,000

1,500

1,500

1,000

1,000

500

500

01.8- 2.8 2.5
3.61.6 -1.9
4.2- 3.8
3.6 2.63.1

J. Biol. Chem.

350
300
250
0.8
0.6
1.3
200
150
1005004.2
4.8- 4.44.2

3 - 3.2
3.6
3.12 0.6
1.8 -1.9
2.5
1.3- 0.8

FEBS J.

0200

Biochem.

4.2
4.8- 4.44.2

2 0.6
3 - 3.2
1.8 -1.9
3.6
3.1 2.5
1.3- 0.8

FEBS Lett.

150
10050
4.2
4.8- 4.4
4.2

2 0.6
3 - 3.2
1.8 - 1.9
3.6
3.1 2.5
1.3- 0.8

04.2
4.8- 4.44.2

2 0.6
3 - 3.2
1.8 - 1.9
3.63.1 2.5
1.3- 0.8

Number of Entries

90807060
50403020100J. Biochem.

3500
3000
2500
2000
1500
1000
500
0J. Biol. Chem.

0.38 0.34 0.30 0.26 0.22 0.18 0.14 0.10

R-factor (Rfree, Rwork)

2000

Biochem.

1500
1000
500
00.40 0.34 0.28 0.22 0.16 0.10

450
400
350
300
250
200
150
100
5002500

FEBS J.

0.40 0.34 0.28 0.22 0.16 0.10

0.40 0.34 0.28 0.22 0.16 0.10

200

FEBS Lett.

150
100
50
00.40 0.34 0.28 0.22 0.16 0.10

実際にやってみますPDBj mine2

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Example1: Gleevec using PDBj-Mine[CASE #3] Chemie searchagainst PDBGleevec ⏎興味のある化合物に結合するタンパク質構造を⾒たい！

29

Explore 1T46: Gleevec using PDBj-Mine (cont.)

30

Eelectron Density map(Molmil)

31

Explore 1T46: Gleevec using PDBj-Mine (cont.)32

実際にやってみます・統計ページ・PDB検索（PDBj Mine2)
・PDB詳細検索
・化合物検索・Sequence-Navigator
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・Molmil[CASE #4] Sequence searchusing BLAST against PDB

1. Select menu
2. SequenceNavigator
相同なタンパク質の構造を調べたい！

[CASE #4] Sequence searchusing BLAST against PDB

1. Select menu
Maize Ferredoxin 1

2. Sequence
Navigator
3. Paste yourtarget sequence
4. Push “Find”button

[CASE #3] Sequence searchusing BLAST against PDB
Result page of the entries
containing “Maize Fd1” will beshown.
①1gaqB = chain B of 1GAQ
②5h8yE = chain E of 3B2F,③5h92C = chain C of 5H92
By clicking the links, we know that
① FNR+Fd1, ② SiR+Fd1, ③SiR+Fd1.

5. Click the link

[CASE #4] Sequence searchusing BLAST against PDB

Summary page of the entry “1GAQ”
will be shown.
This entry contains the electrontransfer complex between Fd1 andFd-NADP+ reductase (FNR).

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Acknowledgements

45