[English] 日本語
Yorodumi
- PDB-1m8l: NMR structure of the HIV-1 Regulatory Protein Vpr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m8l
TitleNMR structure of the HIV-1 Regulatory Protein Vpr
ComponentsVPR Protein
KeywordsVIRAL PROTEIN / Vpr / CD3CN / HIV-1
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / monoatomic ion transmembrane transport / : / virion component / protein homooligomerization / viral penetration into host nucleus / host extracellular space / symbiont entry into host cell / cell cycle / DNA-templated transcription ...symbiont-mediated arrest of host cell cycle during G2/M transition / monoatomic ion transmembrane transport / : / virion component / protein homooligomerization / viral penetration into host nucleus / host extracellular space / symbiont entry into host cell / cell cycle / DNA-templated transcription / host cell nucleus / regulation of DNA-templated transcription
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / Retroviral VpR/VpX protein / VPR/VPX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
AuthorsMorellet, N. / Bouaziz, S. / Lenoir, C. / Roques, B.P.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: NMR Structure of the HIV-1 Regulatory Protein Vpr
Authors: Morellet, N. / Bouaziz, S. / Lenoir, C. / Roques, B.P.
History
DepositionJul 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VPR Protein


Theoretical massNumber of molelcules
Total (without water)11,4121
Polymers11,4121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein VPR Protein


Mass: 11411.905 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is naturally found in human immunodeficiency virus type 1 (HIV-1).
References: UniProt: Q73369

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131HSQC-NOESY
141HSQC-TOCSY
1513D HSQC-NOESY
1613D HSQC-TOCSY
NMR detailsText: This structure was determined using standard 2D and 3D homonuclear and heteronuclear techniques

-
Sample preparation

DetailsContents: 1 mM Vpr 70% H2O, 30% CD3CN pH 2.6 / Solvent system: 70% H2O, 30% CD3CN
Sample conditionspH: 2.6 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
UXNMR3Brukercollection
UXNMR3Brukerdata analysis
Discover98msirefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total 1115 restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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