[English] 日本語
Yorodumi
- PDB-1brv: SOLUTION NMR STRUCTURE OF THE IMMUNODOMINANT REGION OF PROTEIN G ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1brv
TitleSOLUTION NMR STRUCTURE OF THE IMMUNODOMINANT REGION OF PROTEIN G OF BOVINE RESPIRATORY SYNCYTIAL VIRUS, 48 STRUCTURES
ComponentsPROTEIN G
KeywordsGLYCOPROTEIN / ATTACHMENT PROTEIN G OF BOVINE RESPIRATORY SYNCYTIAL VIRUS / IMMUNOGLOBULIN-BINDING PROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / host cell surface / membrane => GO:0016020 / symbiont entry into host cell / virion attachment to host cell / virion membrane / extracellular region
Similarity search - Function
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G
Similarity search - Domain/homology
Major surface glycoprotein G
Similarity search - Component
Biological speciesBovine respiratory syncytial virus
MethodSOLUTION NMR / SEE REMARK 3
AuthorsDoreleijers, J.F. / Langedijk, J.P.M. / Hard, K. / Rullmann, J.A.C. / Boelens, R. / Schaaper, W.M. / Van Oirschot, J.T. / Kaptein, R.
Citation
Journal: Biochemistry / Year: 1996
Title: Solution structure of the immunodominant region of protein G of bovine respiratory syncytial virus.
Authors: Doreleijers, J.F. / Langedijk, J.P. / Hard, K. / Boelens, R. / Rullmann, J.A. / Schaaper, W.M. / van Oirschot, J.T. / Kaptein, R.
#1: Journal: J.Gen.Virol. / Year: 1996
Title: Proposed Three-Dimensional Model for the Attachment Protein G of Respiratory Syncytial Virus
Authors: Langedijk, J.P. / Schaaper, W.M. / Meloen, R.H. / Van Oirschot, J.T.
History
DepositionMar 29, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN G


Theoretical massNumber of molelcules
Total (without water)3,6051
Polymers3,6051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)48 / 50ERROR FUNCTION DGII
Representative

-
Components

#1: Protein/peptide PROTEIN G / / BRSV-G REGION


Mass: 3605.001 Da / Num. of mol.: 1 / Fragment: IMMUNODOMINANT REGION, RESIDUES 158 - 189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine respiratory syncytial virus (strain 391-2)
Genus: Pneumovirus / Species: Bovine respiratory syncytial virus / Strain: 391-2 / References: UniProt: P22261

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131HSQC
141DQF-COSY

-
Sample preparation

Sample conditionspH: 4.6 / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
ManufacturerField strength (MHz)Spectrometer-ID
Varian7501
Bruker5002

-
Processing

NMR software
NameDeveloperClassification
DISCOVERBIOSYMrefinement
REGINEstructure solution
DGIIstructure solution
DISCOVERstructure solution
RefinementMethod: SEE REMARK 3 / Software ordinal: 1
NMR ensembleConformer selection criteria: ERROR FUNCTION DGII / Conformers calculated total number: 50 / Conformers submitted total number: 48

+
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