蛋白質構造データバンク（PDBj）の高度化と統合的運用

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玲、中村 春木 , 鈴木 博文、山下 鈴子、池川 恭代、工藤 高裕、Gert-Jan Bekker,

五十嵐 令子、見学 由美子、張羽澄、佐藤 純子、晴氣 菜穂子、Daron M. Standley, 中川 敦史

Abstract

タ ン パ ク 質、核 酸、糖 鎖 な ど の 生 体 高 分 子 の 立 体 構 造 情 報 は Protein Data Bank(PDB) として集積され、2016 年 6 月には 12 万件を超える構造データを公開している。

Since 2001, PDBj has been managed at Institute for Protein Research, Osaka University as a member of the wwPDB, to curate, edit and process the deposited data
for and open, public, and single archive of the wwPDB. The PDB archive contains more than 123,000 entries now.

PDBj は、国際的組織である wwPDB の一員として、共通した品質管理によるデータ登録作業とダウンロード・サイトの運営および独自のサービス・ツールや二次 DB の提供、セマンティック化を実施している。

● “Data-in” activitiy, common in all the wwPDB members with

これまで、地域による登録サイトの自動振り分け機能等データ登録の高度化と配布を継続的に実施してきた。特に DB の統合的運用を図るため、wwPDB/RDF データを NBDC のRDF ポータルに統合し、特に EBI の PDBe および UniProt グループと協力して SIFTS デー

PDBj staﬀ(April, 2016)

タの RDF 化を実施した。
また、クライオ電子顕微鏡の進展に対応するため、巨大構造も高速に表示できる molmil

PDBj-BMRB staﬀビューアや、PDB、EMDB、SASBDB の 3 つの DB に対して横断的に構造形状の同時比較・

wwPDB since 2003

high quality control. For the purpose, data deposition, validation
system, versioning system, and new format are developed.
● “Data-out” services, common archive as the ftp site andthe characteristic services by each wwPDB member.
120000

検索ができる Omokage 検索 (1) の開発・公開を行った。

100000All available PDB data (123,021, 28 SEP 2016)

PDBj curates and processes

Database Integration

wwPDB/RDF format for Semantic Web

Kinjo et al. (2012) Nucl. Acids Res. 40, D453-D460.
Yokochi et al. (2016) J. Biomed. Semantics, 7:16.
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2)
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d Res. 40,ds
0 D453-D460.
0,

Cryo-EMdata, mainly from Asian andOceania regions .

Integration to NBDC RDF-portal

Service from wwPDB

wwPDB/RDF
http://rdf.wwpdb.org/

80000

about a Quarter of the deposited

wwPDB/RDF format
for
Semantic
Web
Service from wwPDB

Processed total at PDBj (27,779, 27 SEP 2016)

Integration toNBDC RDF-portal

60000

40000

20000

12th Annual wwPDB Advisory Committee meeting
held on 2 Oct 2015 at IPR, Osaka University

0122000

34562005

78910112010

1213141617
*2015
2016

15

*28 SEP 2016

OneDep: New deposition and Annotation system

SAXS

X-ray Structure

BMRB/RDF
http://bmrbpub.protein.osaka-u.ac.jp
Large Complex
NMR Structure

Sequence
Exp. Information(X-ray, NMR, EM, etc)

In UniProt RDF:

PPI (interaction)

NBDC RDF-Portal
https://integbio.jp/rdf/

Integration of PDB data with other databases through SIFTS(Structure integration with function, taxonomy and sequence)

Integration of PDB data with other databases through SIFTS(Structure integration with function, taxonomy and sequence)

PDB Depositions & Annotations
SIFTS
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SIFTS/RDF has been developed collaborating with EBI group based on FALDO(Feature Annotation Location Description Ontology: Bolleman et al, 2016)

Yearly deposited entries
to wwPDB

Collection of ORCID IDs

Yearly deposited entries
to wwPDBOpen Researcher and Contributor ID
http://orcid.org

X-rayNMREM

Example: orcid.org/0000-0001-6690-5863

NMREM

Validation Report withexperimental data
125K

Year

74K 28K 24K

・wwPDB Begins to use in April 2016
・Mandatory going forward in 2018

Large Structures (434) in PDB

M. Ragsac, A.R. Kinjo, H. Nakamura (2016)

Last Updated: 15 September 2015

Large Structures in PDB

Validation Report with experimental data••

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Top page ofValidation report

Molmil: Molecular Viewer based on WebGL
developed by PDBj

Mandatory Experimental data
• X-ray: Structure Factor• NMR: Chemical Shifts and Distance restraints• EM: 3DEM volume map18

Validation report

Molmil: Molecular Viewer based on
WebGL developed by PDBj
Viewing both EM Image and Atomic Structure

Amino acid sequence (FASTA)

Viewing both EM Image
and Atomic Structure

RCSB-PDBThe SIFTS Data (https://www.ebi.ac.uk/pdbe/docs/sifts/quick.html)
are integrated into PDBj Mine and wwPDB/RDF.

• Based on JavaScript/WebGL.
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Data viewer at PDBj
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4v6x: structure ofhuman 80S ribosome,
89 chains, 4 MDa

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EM Navigator: Viewer ofImages of EM-DB

Yorodumi: Viewer of both Image andAtomic Structure

Kinjo et al. NAR 40, D453 (2012)

Characteristic Data-out at PDBj

Characteristic Data-out at PDBj

Omokage search: Search for similar SHAPES in PDB, EMDB and SASBDBAnnotation of Protein Function from MolecularSurface Similarity: eF-site

Protein Molecular Surface DB

Query: human RNA polymerase II with RNA (EMDB: 2190)
Similar shapes from 224,894 images/structures

TRPV1 ion channel by cryo-EM (5irx)

Suzuki, Kawabata, Nakamura (2016) Bioinformatics 32, 619-620