DNA mrna Glycine: G Serine: S Alanine: A Methionine: M Valine: V Phenylalanine: F Aspartic acid: D

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1 DDBJing and PDBjing, : PDBj Protein προτειω prima materia: 1838 J.J. Berzelius (Sweden) Proteome =protein+ ome Genome =gene + ome

2 DNA mrna Glycine: G Serine: S Alanine: A Methionine: M Valine: V Phenylalanine: F Aspartic acid: D

3 (Folding) (Unfolding)

4 Key and Lock model (1MJQ) DNA Tsuchiya et al. (2004) PROTEINS, 55,

6 Protein Data Bank Japan PDB (Protein Data Bank): X (NMR)

7 (PDBj) ProMode ef-site, jv, MrPDB ASH wwpdb (PDBML) PDBj wwpdb XML PDBML

8 PDBj wwpdb XML PDBML : wwpdb (world wide Protein Data Bank) UCSD Rutgers Univ. NIST Research Collaboratory for Structural Bioinformatics NSF Dept. of Energy NIH European Bioinformatics Institute (MSD-EBI) JST- BIRD PDBj wwpdb 2003 (Berman, Henrick & Nakamura (2003) Nat. Struct. Biol. 10, 980)

9 Agreement signature Nature Structure Biology (2003) Vol. 10, No.12

Rutgers Univ. wwpdb RCSB 1) EBI PDBj (RCSB) 2) wwpdb 3) 4) API (Berman, Henrick & Nakamura (2003) Nat. Struct. Biol. 10, 980) RCSB-PDB Team RCSB PDB Team: Ken Addess, Helen M. Berman, Wolfgang F.

10 Rutgers Univ. wwpdb RCSB 1) EBI PDBj (RCSB) 2) wwpdb 3) 4) API (Berman, Henrick & Nakamura (2003) Nat. Struct. Biol. 10, 980) RCSB-PDB Team RCSB PDB Team: Ken Addess, Helen M. Berman, Wolfgang F. Bluhm, Phil Bourne, Kyle Burkhardt, Li Chen, Sharon Cousin, Jim Croker, Nita Deshpande, Shuchismita Dutta, Zukang Feng, Lew-Christiane Fernandez, Judith L. Flippen- Anderson, Gary Gilliland, Rachel Kramer Green, Vladimir Guranovic, Shri Jain, Ann Kagehiro, Charlie Knezevich, Andrei Kouranov, Kevin Lwinmoe, Jeff Merino-Ott, Irina Persikova, Suzanne Richman, Melcoir Rosas, Kathryn Rosecrans, Bohdan Schneider, Wayne Townsend-Merino, Susan Van Arnum, Elizabeth Walker, John Westbrook, Alice Xenachis, Huanwang Yang, Jasmin Yang, Christine Zardecki, Cindy Zhang

Harry Boutselakis search database Dimitris Dimitropoulos MSDChem Joel Fillon ehtpx Adel Golovin active site Kim Henrick group leader Ayzaz Hussain PDB depositions John Ionides NMR / data model

11 Harry Boutselakis search database Dimitris Dimitropoulos MSDChem Joel Fillon ehtpx Adel Golovin active site Kim Henrick group leader Ayzaz Hussain PDB depositions John Ionides NMR / data model Melford John DBA Peter Keller deposition database leader Eugene Krissinel MSDfold Phil McNeil database development Avi Naim EM validation Richard Newman EM / PDB depositions Tom Oldfield search system leader Anne Pajon NMR / data model Jorge Pineda database development Abdel-Krim Rachedi visualization Janet Roser-Copeland outreach Andre Sitnov deposition system Siamak Sobhany API Antonio Suarez-Uruena mapping Jawahar Swaminathan PDB depositions Mohammed Tagari EM / deposition system John Tate search system Swen Tromm validation Sameer Velankar search system Wim Vranken NMR The MSD group at EBI PDBj Members H. Nakamura, M. Kusunoki, Y. Ikegawa, R. Yamashita, Y. Matsuki, A. Paehler, A. Yoshihara, Y. Kengaku, R. Igarashi, Y. Shimizu, A. Takahashi, D. Standley, C. Kamada, S. Saeki, T. Kosada H. Akutsu (Institute for Protein Research, Osaka Univ.) N. Ito (School of Biomedical Science, Tokyo Medical & Dental Univ.) K. Kinoshita (Institute of Medical Science, Univ. Tokyo) H. Wako (Waseda Univ.), S. Endo (Kitasato Univ.) H. Toh (Medical Institute of Bioregulation, Kyushu Univ.) T. Okawa (Kobe Univ.)

12 XX Congress of the International Union of Crystallography at Florence, Aug Kim Henrick, Helen Berman, Haruki Nakamura PDBj wwpdb XML PDBML

14 PDB ADIT Auto Deposition Input Tool Coordinates Str. Factors Precheck Validation check Title Release date Contact author Exp. Condition etc PDB Deposit section End of ADIT input Display PDB id and RCSB id Revised PDB file and Validation letter by an editor Agree or not with the revision Yes Registration Completed No Reply agreement or not within 3 days PDBj Yearly registration number Yearly PDBj registration number Yearly wwpdb registration number Total wwpdb registration number Total registration number year 25% 30%

15 PDBj 1586 ( 5501) Japan: 700 (12.7 % of the world) Austria 7 Korea 47 Belgium 8 Singapore 9 Sweden 20 China: 75 United Kingdom 45 Hong Kong 6 France 68 Taiwan 49 Germany 128 India 62 Denmark 18 Australia 54 Italy 33 New Zealand 17 Netherlands 7 : 1019 Israel 13 Greece 8 Spain 5 USA 97 Switzerland 43 Canada 30 Finland 17 Brazil 5 Czech Republic 1 Mexico 1 Hungary 3 : 133 Poland 3 Portugal 1 Slovenia 6 : 434 PDBj wwpdb XML PDBML

16 PDB CRYST P ORIGX ORIGX ORIGX SCALE SCALE SCALE ATOM 1 N PRO A ATOM 2 CA PRO A ATOM 3 C PRO A ATOM 4 O PRO A ATOM 5 CB PRO A ATOM 6 CG PRO A ATOM 7 CD PRO A ATOM 8 N GLN A ATOM 9 CA GLN A ATOM 10 C GLN A ATOM 11 O GLN A ATOM 12 CB GLN A ATOM 13 CG GLN A ATOM 14 CD GLN A ATOM 15 OE1 GLN A ATOM 16 NE2 GLN A X Y Z =10-8 cm PDB A-91B ( ) ( ) (flexible )

PDBML: canonical XML description of PDB data, developed by the wwpdb. (Westbrook et al. (2005) Bioinformatics, 21, 988-992) No validation errors for more than 34,000 PDB file description.

17 PDBML: canonical XML description of PDB data, developed by the wwpdb. (Westbrook et al. (2005) Bioinformatics, 21, ) No validation errors for more than 34,000 PDB file description. PDBML ATOM 1 N THR A PDB-format <PDBx:atom_siteCategory> <PDBx:atom_site id="1"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_entity_id>1</PDBx:label_entity_id> <PDBx:label_seq_id>1</PDBx:label_seq_id> <PDBx:Cartn_x>17.047</PDBx:Cartn_x> Full-tag (all) <PDBx:Cartn_y>14.099</PDBx:Cartn_y> <PDBx:Cartn_z>3.625</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>13.79</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>1</PDBx:auth_seq_id> <PDBx:auth_comp_id>THR</PDBx:auth_comp_id> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>N</PDBx:auth_atom_id> <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num> </PDBx:atom_site> (ext-atom) <atom_record id="1">atom 1 A A 1 1?. THR THR N N N </atom_record>

18 12as : * *2as, 12*, *

19 As* and synthetase and *

20 Jv3

24 12AS(Asn Synthetase) XPath

25 12AS(Asn Synthetase) XPath SOAP (Simple Object Access Protocol) example %./sample1.pl 50 <struct_site_gen auth_validate="n" info_subtype="catalytic" info_type="catres" ino:id="71" nid="1" site_id="catres1" update_id="1" xmlns:xsi=" <label_comp_id>arg</label_comp_id> <label_asym_id>a<label_asym_id></label_asym_id> <label_seq_id>100<label_seq_id></label_seq_id> <details>transition-state stabilisation. stabilise negatively charged tetrahedral intermediate</details> </struct_site_gen> <struct_site_gen auth_validate="n" info_subtype="catalytic" info_type="catres" ino:id="71" nid="2" site_id="catres1" update_id="1" xmlns:xsi=" <label_comp_id>asp</label_comp_id> <label_asym_id>a<label_asym_id></label_asym_id> <label_seq_id>46<label_seq_id></label_seq_id> <details>acid/base, transition-state stabilisation. stabilises positively charged NH3+ part of intermediate, then as a base removes proton from this, leading to collapse and formation of asn</details> </struct_site_gen> <struct_site_gen auth_validate="n" info_subtype="catalytic" info_type="catres" ino:id="71" nid="3" site_id="catres1" update_id="1" xmlns:xsi=" <label_comp_id>gln</label_comp_id> <label_asym_id>a<label_asym_id></label_asym_id> <label_seq_id>116<label_seq_id></label_seq_id> <details>transition-state stabilisation. stabilise negatively charged tetrahedral intermediate</details> </struct_site_gen>

PDBjViewer or jv RasMol ( ). JAVA XML PDBML all & ext-atom http://www.

26 PDBjViewer or jv RasMol ( ). JAVA XML PDBML all & ext-atom xpsss Database System xpsss Manual input from literatures

27 PDBj wwpdb XML PDBML PDB PDB XML

28 xpsss PDBML 34,065 GO (Genome Ontology) (Biological Process, Molecular Function, Cellular Component) 15,728 HETATM SwissProt (UniProt) 23,838 (ACT_SITE, BINDING, DNA_BIND, NP_BIND, ZN_FING, TRANSMEM) Prosite CATRES/extCATRES EBI- 2,797 CSA-EBI- 11,066 PubMed 25,392 17,705 15,160 26,765 as of December 8, 2005 <exptl> <method>synchrotron RADIATION</method> <crystal id="1"> <grow auth_validate="n" update_id="6"> <method auth_validate="n" update_id="6">microdialysis</method> <temp auth_validate="n" unit="℃" update_id="6">4</temp> <ph auth_validate="n" update_id="6">4</ph> </grow> <grow_comp id="1" auth_validate="n" update_id="6"> <sol_id auth_validate="n" update_id="6">1</sol_id> <name auth_validate="n" type="common name" update_id="6">protein</name> <conc auth_validate="n" unit="mg/ml" update_id="6">13</conc> </grow_comp> <grow_comp id="2" auth_validate="n" update_id="6"> <sol_id auth_validate="n" update_id="6">2</sol_id> <name auth_validate="n" type="common name" update_id="6">ammonium sulphate</name> <conc auth_validate="n" unit="%sat" update_id="6">70</conc> </grow_comp> : : </crystal> </exptl>

<struct> <site id="catres1" auth_validate="n" info_subtype="catalytic" info_type="catres" update_id="2"> <num_residues>3</num_residues> <details>a catalytic site defined by CATRESS, Medline

29 <struct> <site id="catres1" auth_validate="n" info_subtype="catalytic" info_type="catres" update_id="2"> <num_residues>3</num_residues> <details>a catalytic site defined by CATRESS, Medline </details> <site_gen nid="1"> <label_comp_id>arg</label_comp_id> <label_asym_id>1</label_asym_id> <label_seq_id>100</label_seq_id> <details>transition-state stabilisation. stabilise negatively charged tetrahedral intermediate</details> </site_gen> <site_gen nid="2"> <label_comp_id>asp</label_comp_id> <label_asym_id>1</label_asym_id> <label_seq_id>46</label_seq_id> <details>acid/base, transition-state stabilisation. stabilises positively charged NH3+ part of intermediate, then as a base removes proton from this, leading to collapse and formation of asn</details> </site_gen> <site_gen nid="3"> <label_comp_id>gln</label_comp_id> <label_asym_id>1</label_asym_id> <label_seq_id>116</label_seq_id> <details>transition-state stabilisation. stabilise negatively charged tetrahedral intermediate</details> </site_gen> </site> </struct>

31 Example for 12as with the functional site information Advanced usage of jv version3 with xpsss Command: show xps3

33 PDBj wwpdb XML PDBML Development of Secondary Databases: data mining Protein Molecular Surface Database, ef-site (Kinoshita & Nakamura Protein Dynamics Database, ProMode (Wako & Endo) Alignment of Structural Homologues, ASH (Toh) Sequence Navigator & Structure Navigator (Standley Encyclopedia of Protein Structures, eprots (Ito & Nakamura

ef-site database for Ligand recognition sites www.pdbj.

34 ef-site database for Ligand recognition sites /ef-site/ Kinoshita, Furui, Nakamura (2002) J. Struct. Funct. Genomics 2, Kinoshita, Nakamura (2004) Bioinformatics 20,

35 Displayed with the jv applet

38 ASH: Alignment of Structural Homologues

40 NER: Number of Equivalent Residues Standley, Toh, Nakamura (2004) PROTEINS 57,

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PowerPoint プレゼンテーション DDBJing and PDBjing, 2005 年 3 月 2 日日本蛋白質構造データバンク : PDBj の紹介と HP の使い方中村春木大阪大学蛋白質研究所附属プロテオミクス総合研究センター蛋白質情報科学研究室 http://www.pdbj.org/ PDBj Protein Data Bank Japan http://www.pdbj.org/ 大阪大学蛋白質研究所にて実施 (