16 & 17 October 2008

IMSS Symposium:
Structural Biology
Research Center
6.5GeVPF-AR

2.5 GeV PF

Soichi Wakatsuki
Photon Factory
Institute of Materials Structure
ScienceHigh Energy Accelerator
Research Organization (KEK)Crystallization
200,000 trials/day

Structural Biology
Research Center

Modified SSRL sample
changer robot

L in a c

StructuralBiology
Research Center
6.5GeV PF-AR

2.5GeVPF ring

NW12A (2003)

BL-6A

BL-5A (2004)

BL-17A (2006)

SSRL-type robot installed on MAD Beamline BL-5
20 datasets/day ⇒ 100s datasets/day
4-axis Robot
Monitoring Camera
Force Sensor
Cryo TongSample
GoniometerLN2 Dewar

CCD Detector

Double Tong

Cryo Nozzle

Cassettes

Fancy Box

Compatible with SSRL（USA）, SRRC（Taiwan）& AS (Australia), CLS (Canada)
Compatibility with SPring-8 and European
standards being worked

High precision one axis diffractometers with XYZ stages
BLBL-6A

NW12

BL-5

BL-17

Year started

2000*2003

2004

2006

Max deviation（µm）

102.2

1.00.37(2007)⇒ 0.1(2009)

Xtal size （µm）

100

22

104 (2007) ⇒ 1 (2009)"#$345,-672"#%

0.36µm"#&0.6 mm"!"#&!"#%!"#$Air bearing & magnetic x-y stages"'""&"")*+,-./01//2

BL-5 type diffractometer -> also installed on BL41XU & BL44XU, SPring8(""No. of Beam Time Proposals on Protein Crystallography Beam Lines at PF
Doubled in the last 7 years.
$"!

/0012'1)%34525&67&

89:%5;%<9((=(>%34525&67&$!!

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!#%#&'!#$()!$%#&'!$$()!*%#&'!*$()!+%#&'!+ !"%#&' !" !,%#&' !, !-%#&' !- !.%#&'
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“Flipping-out” mechanism of recognition ofhemi-methylated DNA by UHRF1 (BL-5A)
by M. Shiraka’s group, Kyoto University
K. Arita et al., Nature, 455, 818-821 (2008).

DNA methylation is an important epigenetic modification of mammalian genomes andessential for the gene expression. Inheritance of the methylation pattern is mediatedby the enzyme Dnmt1, and the protein UHRF1 recognizes hemimethylation sites anddirects Dnmt1 to these sites. Crystal structure of the complex of DNA and SRA
domain of UHRF1 revealed that the hemi-metylated site is flipped out of the DNAhelix.

Structural basis for specific cleavage ofLys 63-linked polyubiquitin (NW12A)
S. Fukai’s group, Tokyo Univ., Res. Org. Sync. Rad.
Y. Sato et al., Nature, 455, 358-362 (2008).

Ubiquitin is a post-translational modifier that regulates a wide variety of biologicalprocesses. Lys 48-linked polyubiquitin chains are the most abundant linkage in vivo
and constitute the signal for degradation by the proteasome. However, Lys 63-linked
polyubiquitin chains serve proteasome-independant roles. The structure of AMSH
family members which specifically cleave Lys 63-linked polyubiquitin chain wasdetermined.

Essential subunit interaction in influenza
virus RNA polymerase (BL-5A)
S. Park’s group, Yokohama City University
E. Obayashi et al., Nature, 454, 1127-1131 (2008).

Influenza virus is a major human and animal pathogen, and reproduces rapidly,
mutates frequently and occasionally crosses species. The importance to viral
replication of a subunit interface in the viral RNA polymerase was demonstrated by
the crystal structure. The structure presented here provide a new set of potential drug
binding sites.

Protein 3000 (Ministry of Education, Culture, Sports, Science and Technology)
Network Committee forProtein Analyses
500〜600 structures, R&D,
Structure-Function,Education
Transcription andTranslation

RIKEN
RIKEN Structural Genomics/Proteomics
Initiative (RSGI)（2500 structures、Structure.-Function、R&D）

Corporation instructuralgenomics R&D

Yokohama Genome Science Center
Harima Institute

OtherInstitutions

Collaboration
Collaboration

Development and Cell
Differentiation
Protein Transport andModification

Osaka Univ.
Inst. for Protein
Research

Other ResearchCenters of RIKEN
Beam time use

Collaboration

Collaboration
Collaboration

Beam time use

Signal Transduction
SPring-8
Higher Order BiologicalFunctions
Brain and Neurology

Beam time useCorporation
in R&D andfacility
operationPhoton Factory
Beam time use

Metabolism
Collaboration

Industry

Protein 3000 Tsukuba Structural Biology Consortium (21 groups)
Protein Transport and Posttranslational Modification
Showa Univ (PX)

KEK, Photon Factory (PX, SAXS)
Nagaoka Tech Univ (X-ray)
Nara Inst. Sci. & Tech (SAXS)

Nagoya City Univ. (NMR)

Tokyo Inst. Tech (PX)JAERI, Nara (Bioinfo)

Original goal: 70 in 5 years (2003-March 2007)⇒ changed to 150 in the second year
254 structures solved (31 March 2007)
Osaka University
Inst. Microbial Diseases
Kyoto University
Pharmacology Department
NAIST,Molecular Biology Lab
Kyoto University
Life Science Program

171 PDB deposits

Kagoshima University
Medical School

University of Tokyo (Komaba)

Riken, Membrane
Traffic Group

Osaka University
Medical School
Tokyo Metropolitan
Institute of Gerontology

RikenImmunology InstituteKyoto Sangyo University
Faculty of Engineering

Endocytosis of toxin -> Drug delivery

David S. Goodsell, Scripps Institute, http://www.scripps.edu/mb/goodsell/Human GGA: a new class of adaptor proteins
GATClathrin
terminal domain① VHSClathrin

GAE
M6PR

MPR

③

ARF-GTP②
N-GAT

Accessory protein

clathrin box
Hinge region

TGN membraneLumen① Shiba et al. Nature 415,937-941, 2002cargo protein
Shiba et al., Traffic, vol. 5, 437-448, 2004
② Shiba et al., Nature Structural Biology, 10 386-393, 2003
Shiba et al., J. Biol. Chem. 279, 7105-11279, 2004
Kawasaki et al., Genes to Cells, 10, 639–654, 2005
Yogosawa et al., BBRC, 350, 82-90, 2006
③ Nogi et al. Nature Structural Biology, 9, 527-531, 2002
Inoue et al. Traffic, 8, 904-913, 2007

Protein complexes necessary
for the melanosome trafficking

M. Kukimoto-Niino
et al., Structure,16, 1478-1490(2008).
SP8 BL41XU

Review by R.
Goody,Structure, 16,1437-1439(2008).

L.M.G.
Chavas etal., Structure,
16, 14681477 (2008).
PF BL-5A

Joint Press Release
by RIKEN and KEK
on Oct 3rd, 2008

Structure Based Drug Design：more efficient and lower cost for development of
Anti influenza drug with little or no side effects (collab. with Italy, Australia, Canada)
Influenza neuraminidase

Tamiflu
derivedLead compounds

Zanamivir。
Inhibitor design

Clinical tests
Selection

Active site

Drugs with noside effects:
Interaction with
only influenza
neuraminidase
but NOT withhuman sialidases

Structure Determination using SR
Tamiflu
DifferenceYellow: human sialidase Neu2
Gray: Influenza neuraminidase

Human sialidase
Neu2 structure

Side effects:
Humansialidases?
Neu1, Neu2,Neu3, Neu4

Industrial Use and Collaborations
between KEK and Industry (~8% of beamtime)

MX BLs at Photon Factory

Ajinomoto Co., Inc
Astellas Pharma Inc.

Astellas Pharma.
Beam Line ARNE3 (to becompleted byMarch 2009)
Company ①Company ②
Astellas ③

Tsukuba StructuralBiology
Consortium for
IndustrialApplications（sinceApril 1, 2006）
Pharmaceutical
Consortium for Protein
Structure Analysis(PCProt), Japan
Pharmaceutical
Manufacturers Association(JPMA)
BL32B2 at SPring8Eizai Co. Ltd.
KYOWA HAKKOKOGYO Co., LTD.
DAIICHI SANKYO
Co. Ltd.
CHUGAI
PHARMACEUTICAL
Co., Ltd.
BANYU
PHARMACEUTICAL
Co., Ltd.
Mitsubishi ChemicalCorporation
New members

Astellas Pharma Beam
Line: PF-AR NE3 New
Available from Apr. 2009

NE3 Undulator

Optics Hutch
CM DCM FMFPExp. Hutch• Expected to become stronger than AR-NW12A• Astellas Pharma will have priority access for certain
amount of beam time during 10 years from April 2009.
• The rest of the beam time can be used for generaluser operation including use by other pharmaceuticalcompanies.Photon Factory

MEXT: Target Protein Project(2007-2011)

SPring-8

Joint Proposal by SPring-8 and PF:
Two Complimentary New Beam LinesPF② Microfocus
Beam Line
Low to medium
energy (Invacuumshort gapundulator)
1.
2.
3.

① Microfocus
Beam Line
Medium to highenergyTo be completed by end of March 2009
Compatibility: SPring-8 and PF robots
Remote access and control

In collaboration with Hokkaido Univ, Kyoto
Univ, and Osaka Univ.

SPring-8

Collaboration outside of Japan
1. Human sialidase: G. Tattamanti & G. Monti, Italy,(Chavas et al., J. Biol. Chem., 2005)
2. Human sialidase inhibitors: M.v. Itzstein, Institutefor Glycomics, Griffith University, Australia
3. Sialidase inhibitors: Peter Colman, Australia
Steve Withers, Canada
4. Endocytic pathways: H. Stenmark, Oslo, Norway(Slagsvold et al. J. Biol. Chem., 2005, Hirano et al. Nature
Struct. Mol. Biol. 13, 272, 2006, Hirano et al. Nature
Struct. Mol. Biol. 13, 1031, 2006)
5. Protein carbohydrate recognition in HIV infection:
R. Varadarajan, Bangalore, India
6. Protein carbohydrate interaction, Johan Deisenhofer,Univ. Texas, USA (C.-I. Chang et al. PNAS, June 2005)
7. Ubiquitin recognition, Ivan Dikic, Johan Wolfgan Goethe
Univ., Frankfurt, Germany, to be submitted to NatureAcknowledgements
SPring-8
Masaki Yamamoto’s group
Hokkaido University
Isao Tanaka
Kyoto University
Kunio Miki
Osaka University
Atsushi Nakagawa
Mamoru Suzuki
Nagoya University
Nobuhisa Watanabe

Financial Supports
Development of Systems andTechnology for Advanced
Measurement and Analysis(JST)
Protein 3000 Project (MEXT)Grand-in-Aid for Young
Scientists (B) 18770098(MEXT)
Target Protein Research
Program (MEXT)

Structural Biology Research Center, Photon Factory, KEK
Soichi Wakatsuki

Professor, Director of Structural Biology Research Center

Structural Biology
Ryuchi Kato (Associate Prof.)
Masato Kawasaki (Research Assoc.）
Kentaro Ihara （Post Doc Fellow）
Norio Kudo （Post Doc Fellow）
Mohammad Yousef (JSPS fellow)
Tamami Uejima（Researcher）
Tamie Aoki（Lab Technician）
Honda （Lab Technician）
Ex members:
Tadashi Satoh （Post Doc Fellow）
Leonard Chavas (Post Doc Fellow)+++Beamline & Robotics
Noriyuki Igarashi （Research Assoc.）
BL-6A, BL-17
Naohiro Matsugaki （Res. Assoc.）
AR-NW12, BL1
Masashiko Hiraki （Res. Assoc.）
Robotics
Yusuke Yamada （Research Assoc.）
NE3
Yurii Gaponov （Researcher） Programming
Kumiko Sasajima（System Engineer）
Shokei Watanabe （Mechanical Engineer）
Nobuo Honda（System Engineer）
Kazutaka Demura（Beamline Assistant）
Kubota （Beamline Assistant）

The Graduate University for Advanced Studies
Junichi Kouyama (D4), Simin Rahigi (D2), Ahmed Rohaim(D1), Kensuke Nakamura (M1), Ken Ohkubo (M1)

Secretaries
Naomi Nagata*
Tomoko Zeniya*
Ritsuko Ebisawa*
Reiko Sukegawa

Internship Students: Atsuko Tsuchiya (Kyoto Univ. M1), Ryunosuke Nakatani (Nagaoka Univ. of Tech. B4)

16 October 2008

Thank you for yourattention.
6.5GeVPF-AR

2.5 GeV PF