[English] 日本語
Yorodumi
- PDB-2fvn: The fibrillar tip complex of the Afa/Dr adhesins from pathogen E.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fvn
TitleThe fibrillar tip complex of the Afa/Dr adhesins from pathogen E. coli displays synergistic binding to 5 1 and v 3 integrins
ComponentsProtein afaD
KeywordsCELL ADHESION / afaD / afaE / fibrillar / afimbrial / integrin-binding / DAEC / DAF / CEACAM
Function / homologyEnterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Protein AfaD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Aria-implemented distance geometry, simulated annealing
AuthorsCota, E. / Simpson, P. / Anderson, K.L. / Matthews, S.J.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: The solution structure of the invasive tip complex from Afa/Dr fibrils
Authors: Cota, E. / Jones, C. / Simpson, P. / Altroff, H. / Anderson, K.L. / du Merle, L. / Guignot, J. / Servin, A. / Le Bouguenec, C. / Mardon, H. / Matthews, S.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein afaD


Theoretical massNumber of molelcules
Total (without water)16,6301
Polymers16,6301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -REGULARIZED MEAN STRUCTURE
Representative

-
Components

#1: Protein Protein afaD


Mass: 16630.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q47038
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM afaD-dsc, U-15N, 13C; 50mM Na phosphate buffer(pH 7.0); 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM afaDE-dsc, U-15N, 13C, D2O; 50mM Na phosphate buffer(pH 7.0); 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate / pH: 7 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue, Nilgesrefinement
ARIA1.2Linge, O'Donoghue, Nilgesstructure solution
NMRView4Johnson, Blevinsdata analysis
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
XwinNMR3.1Bruker Biospincollection
RefinementMethod: Aria-implemented distance geometry, simulated annealing
Software ordinal: 1
Details: Structure based on 3839 noe-based restraints (2951 unambiguous, 1423 ambiguous) and 116 torsion angles (talos)
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers submitted total number: 1

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more