[English] 日本語
Yorodumi
- PDB-1ceu: NMR STRUCTURE OF THE (1-51) N-TERMINAL DOMAIN OF THE HIV-1 REGULA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ceu
TitleNMR STRUCTURE OF THE (1-51) N-TERMINAL DOMAIN OF THE HIV-1 REGULATORY PROTEIN
ComponentsPROTEIN (HIV-1 REGULATORY PROTEIN N-TERMINAL DOMAIN VPR)
KeywordsVIRAL PROTEIN / REGULATORY PROTEIN / HELICAL DOMAIN / AMPHIPATICITY
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 / cell cycle / symbiont entry into host cell / 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 / cell cycle / symbiont entry into host cell / DNA-templated transcription / host cell nucleus / regulation of DNA-templated transcription
Similarity search - Function
Hiv-1 Regulatory Protein N-terminal Domain Vpr; Chain: A; / Hiv-1 Regulatory Protein N-terminal Domain Vpr; Chain: A; - #10 / Retroviral VpR/VpX protein / VPR/VPX protein / Helix non-globular / Special
Similarity search - Domain/homology
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING, MOLECULAR DYNAMICS, ENERGY MINIMIZATION
AuthorsWecker, K. / Roques, B.P.
CitationJournal: Eur.J.Biochem. / Year: 1999
Title: NMR structure of the (1-51) N-terminal domain of the HIV-1 regulatory protein Vpr.
Authors: Wecker, K. / Roques, B.P.
History
DepositionMar 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (HIV-1 REGULATORY PROTEIN N-TERMINAL DOMAIN VPR)


Theoretical massNumber of molelcules
Total (without water)6,1731
Polymers6,1731
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 / 16LEAST RESTRAINT VIOLATIONS, LOWEST TOTAL ENERGY
Representative

-
Components

#1: Protein PROTEIN (HIV-1 REGULATORY PROTEIN N-TERMINAL DOMAIN VPR)


Mass: 6172.783 Da / Num. of mol.: 1 / Fragment: 1-51 / Source method: obtained synthetically
Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED BY SOLID PHASE SYNTHESIS. THE SEQUENCE OF THIS PROTEIN IS FOUND IN THE VPR GENE, HIV-1 LAI ISOLATE VARIANT OF V6750.
References: UniProt: Q73369

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131E.COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H-NMR SPECTROSCOPY ON THE N-TERMINAL DOMAIN (1-51)VPR.

-
Sample preparation

Sample conditionspH: 3.4 / Pressure: 1 atm / Temperature: 323 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
BUXNMRBRUKERstructure solution
BIOSYM/MSI FELIXstructure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING, MOLECULAR DYNAMICS, ENERGY MINIMIZATION
Software ordinal: 1
Details: FIFTY STRUCTURES WERE GENERATED BY SIMULATED ANNEALING AND ENERGY MINIMIZATION. THE BEST STRUCTURE SELECTED WITH RESPECT TO RESTRAINT VIOLATIONS AND TOTAL ENERGY IS PRESENTED IN THIS ENTRY.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS, LOWEST TOTAL ENERGY
Conformers calculated total number: 16 / 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