[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleA Distinct Type of Pilus from the Human Microbiome.
Journal, issue, pagesCell, Vol. 165, Page 690-703, Year 2016
Publish dateJan 25, 2010 (structure data deposition date)
AuthorsXu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. ...Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Curtis, M.A. / Nakayama, K. / Wilson, I.A.
External linksCell / PubMed:27062925
MethodsX-ray diffraction
Resolution1.3 - 3 Å
Structure data

PDB-3liu:
Crystal structure of Putative cell adhesion protein (YP_001304840.1) from Parabacteroides distasonis ATCC 8503 at 2.05 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-3pay:
Crystal structure of a putative adhesin (BACOVA_04077) from Bacteroides ovatus at 2.50 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-3r4r:
Crystal structure of a fimbrial assembly protein (BDI_3522) from Parabacteroides distasonis ATCC 8503 at 2.38 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-3sy6:
Crystal structure of a fimbrial protein BF1861 [Bacteroides fragilis NCTC 9343] (BF1861) from Bacteroides fragilis NCTC 9343 at 1.90 A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3t2l:
Crystal structure of a Putative cell adhesion protein (BF1858) from Bacteroides fragilis NCTC 9343 at 2.33 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.33 Å

PDB-3ufi:
Crystal structure of a putative cell adhesion protein (BACOVA_04980) from Bacteroides ovatus ATCC 8483 at 2.18 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.18 Å

PDB-3up6:
Crystal structure of a putative cell adhesion protein (BACOVA_04078) from Bacteroides ovatus ATCC 8483 at 2.80 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-4dgu:
Crystal structure of a putative cell adhesion protein (BT0320) from Bacteroides thetaiotaomicron VPI-5482 at 2.37 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-4eps:
Crystal structure of a fimbrial protein (BACOVA_04982) from Bacteroides ovatus ATCC 8483 at 1.85 A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-4gpv:
Crystal structure of a putative cell adhesion protein (BACEGG_00536) from Bacteroides eggerthii DSM 20697 at 1.67 A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-4h40:
Crystal structure of a putative cell adhesion protein (BF2867) from Bacteroides fragilis NCTC 9343 at 2.57 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.57 Å

PDB-4jg5:
Crystal structure of a putative cell adhesion protein (BDI_3519) from Parabacteroides distasonis ATCC 8503 at 2.34 A resolution (PSI Community Target, Nakayama)
Method: X-RAY DIFFRACTION / Resolution: 2.34 Å

PDB-4jrf:
Crystal structure of a putative cell adhesion protein (BACOVA_01548) from Bacteroides ovatus ATCC 8483 at 1.98 A resolution (PSI Community Target, Nakayama)
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-4k4k:
Crystal structure of a putative cell adhesion protein (BACUNI_00621) from Bacteroides uniformis ATCC 8492 at 1.67 A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-4q98:
Crystal structure of a fimbrilin (fimA) from Porphyromonas gingivalis W83 at 1.30 A resolution (PSI Community Target, Nakayama)
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-4qb7:
Crystal structure of a fimbrial protein (BVU_2522) from Bacteroides vulgatus ATCC 8482 at 2.55 A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-4qdg:
Crystal structure of a putative adhesin (BT2657) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution (PSI Community Target, Nakayama)
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-4rdb:
Crystal structure of an immunoreactive 32 kDa antigen PG49 (PG_0181) from Porphyromonas gingivalis W83 at 1.45 A resolution (PSI Community Target, Nakayama)
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-5cag:
Crystal structure of a putative adhesin (BACOVA_02677) from Bacteroides ovatus ATCC 8483 at 3.00 A resolution (PSI Community Target, Nakayama)
Method: X-RAY DIFFRACTION / Resolution: 3 Å

Chemicals

ChemComp-CL:
Unknown entry

ChemComp-GOL:
GLYCEROL

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-NHE:
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / pH buffer*YM

ChemComp-ZN:
Unknown entry

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-CA:
Unknown entry

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-NA:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-ACN:
ACETONE

Source
  • parabacteroides distasonis (bacteria)
  • bacteroides ovatus (bacteria)
  • bacteroides fragilis (bacteria)
  • bacteroides thetaiotaomicron (bacteria)
  • bacteroides eggerthii (bacteria)
  • bacteroides uniformis (bacteria)
  • porphyromonas gingivalis (bacteria)
  • bacteroides vulgatus (bacteria)
KeywordsCELL ADHESION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / PSI-BIOLOGY / transthyretin-like (also known as prealbumin-like) / FIMBRIAL PROTEIN / ADHESION / Prealbumin-like fold / Major fimbrial subunit protein (FimA) / Cell adhesion protein / fimbrial related protein / Unknown Function / HYPOTHETICAL PROTEIN (DUF3988) / PF06321 family / Fimbriae like protein / PF08842 family / Fimbrillin-like protein / PF13149 family / DUF3988 / PF06321 / Type IV / PF15495 / Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 / Putative cell adhesion protein / PF16249 family / DUF4906 / adhesin

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more