蛋白質構造データバンク（PDBj）の検証高度化と統合化

http://pdbj.org/○栗栖源嗣，中川敦史，鈴木博文，金城

http://wwpdb.org/

玲，中村 春木

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、2017 年 10 月には 13 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 datafor and open, public, and single archive of the wwPDB. The PDB archive contains more than 133,000 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PDBj staﬀ
(April, 2017)

マンティック化を実施している。

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

これまでに、PDB コンテンツのセマンティック化が実施済みである。本年度から開始した
新しい研究課題では、今後ますます重要となるデータ検証レポートのセマンティック化と5"#6,.,7&',2"#$&'34&!"#!"#+)(,-.,'!"#$#)*/"0"#1,'.()*

その応用を実施し、利用者がゲノム等の他のデータベースとの統合的な利用の際に活用できる仕組みを構築する。さらに、分子内及び分子間の原子レベルないし残基レベルの相互作用情報を適切なオントロジーを付して RDF として公開することを目指し、製薬企業での化合物スクリーニングの際に PDB と併用される基盤化学データベースである CSD との統wwPDB since 2003

合化も進める。
PDBj-BMRB staﬀ

Database Integration

Integration to NBDC RDF-portal

Service from wwPDB

wwPDB/RDF format
forSemantic
Web
Service from wwPDB
Kinjo et al. (2012) Nucl. Acids Res. 40, D453-D460.
Yokochi et al. (2016) J. Biomed. Semantics, 7:16.
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Cryo-EM

Integration toNBDC RDF-portal

wwPDB sumit, May 2017

PDBj curates and processes

100000data, mainly from Asian andmiddle east regions .

80000
60000
40000
20000
02000

2005

2010

2015 2017

OneDep: New deposition and Annotation system

SAXS

X-ray Structure

BMRB/RDF
http://bmrbpub.protein.osaka-u.ac.jp

120000

about a Quarter of the deposited

wwPDB/RDF format for Semantic Web

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

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.
140000Large Complex

NMR Structure

SequenceExp. 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

PDB Depositions & Annotations

SIFTS
ftp://ftp.pdbj.org/RDF/sifts/•SIFTS/RDF has been developed collaborating with EBI group based on FALDO(Feature Annotation Location Description Ontology: Bolleman et al, 2016)

As of 2016 region-based
processing of D&Adeposited entries:– RCSB PDB: Americas &Oceania– PDBe: Europe & Africa– PDBj: Asia & Middle East

Yearly deposited entries
to wwPDB

Collection of ORCID IDs

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

X-ray
NMR

EM

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

NMR
EM

Validation Report withexperimental data

Year・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)

Large Structures in PDB

Validation Report with experimental data••As of December 2014, large structures are no longer split into multiple
PDB entries but are released as single PDBx/mmCIF and PDBML files– Existing split entries were consolidated into single entries– A bundle of best-effort PDB files (PDB bundle) is available for everylarge structure through the wwPDB FTP sites
Each wwPDB member provides tools to view large structures
PDBePDBj

PDBj Services
Data–out from PDBj
Data–out from PDBj
http://pdbj.org/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 map

18

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 Imageand Atomic Structure•••••

Data viewer at PDBj
Graphic viewer: jV andMolmil
http://pdbj.org/jV/

Molecular surface DB: eF-sitee
http://ef-site.hgc.jp/eF-site/

4v6x: structure ofhuman 80S ribosome,
89 chains, 4 MDa

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.
Supports PDB, mmCIF, PDBML formats.
Links to PDB, chem_comp （Compound）, eF-site, andProMode Elastic.
Outputs screenshots.
Available for iOS8, iOS9 (iPAD, iPhone etc)
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-siteProtein 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