[English] 日本語
Yorodumi
- PDB-2nef: HIV-1 NEF (REGULATORY FACTOR), NMR, 40 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nef
TitleHIV-1 NEF (REGULATORY FACTOR), NMR, 40 STRUCTURES
ComponentsNEGATIVE FACTOR (F-PROTEIN)
KeywordsREGULATORY FACTOR / AIDS / MYRISTYLATION / GTP-BINDING
Function / homology
Function and homology information


symbiont-mediated suppression of host T-cell mediated immune response / symbiont-mediated suppression of host adaptive immune response / negative regulation of CD4 production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / virion component => GO:0044423 / suppression by virus of host autophagy / CD4 receptor binding / thioesterase binding / host cell Golgi membrane ...symbiont-mediated suppression of host T-cell mediated immune response / symbiont-mediated suppression of host adaptive immune response / negative regulation of CD4 production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / virion component => GO:0044423 / suppression by virus of host autophagy / CD4 receptor binding / thioesterase binding / host cell Golgi membrane / MHC class I protein binding / : / regulation of calcium-mediated signaling / viral life cycle / SH3 domain binding / ATPase binding / signaling receptor binding / GTP binding / protein kinase binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR
AuthorsGrzesiek, S. / Bax, A. / Clore, G.M. / Gronenborn, A.M. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Tjandra, N. / Wingfield, P.T.
Citation
Journal: Protein Sci. / Year: 1997
Title: Refined solution structure and backbone dynamics of HIV-1 Nef.
Authors: Grzesiek, S. / Bax, A. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Tjandra, N. / Wingfield, P.T.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: The Solution Structure of HIV-1 Nef Reveals an Unexpected Fold and Permits Delineation of the Binding Surface for the SH3 Domain of HCK Tyrosine Protein Kinase
Authors: Grzesiek, S. / Bax, A. / Clore, G.M. / Gronenborn, A.M. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Wingfield, P.T.
History
DepositionFeb 12, 1997Processing site: BNL
SupersessionJul 7, 1997ID: 1NEF
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEGATIVE FACTOR (F-PROTEIN)


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
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)40 / -
Representative

-
Components

#1: Protein NEGATIVE FACTOR (F-PROTEIN) / HIV-1 NEF


Mass: 16148.163 Da / Num. of mol.: 1 / Mutation: DEL(2-39), DEL(159-173), C206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: BH10 / Gene: HIV-1 NEF / Plasmid: PET11A / Gene (production host): HIV-1 NEF / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q70627
Sequence detailsTHE MATERIAL USED WAS A DELETION MUTANT: DELTA 2 - 39 AND DELTA 159 - 173, WHICH REMOVES THE ...THE MATERIAL USED WAS A DELETION MUTANT: DELTA 2 - 39 AND DELTA 159 - 173, WHICH REMOVES THE DISORDERED N-TERMINUS AND REDUCES THE SIZE OF A LONG DISORDERED SOLVENT EXPOSED LOOP. IT ALSO CONTAINS A CYS 206 TO ALA MUTATION TO PREVENT THE FORMATION OF INTERMOLECULAR DISULFIDES. THE HIV-1 STRAIN FROM WHICH THE PROTEIN WAS DERIVED IS STRAIN BH10.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE 3D STRUCTURE OF THE HIV-1 NEF (DELTA2 - 39, DELTA 159 - 173) SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 1250 EXPERIMENTAL RESTRAINTS: 338 SEQUENTIAL (|I- ...Text: THE 3D STRUCTURE OF THE HIV-1 NEF (DELTA2 - 39, DELTA 159 - 173) SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 1250 EXPERIMENTAL RESTRAINTS: 338 SEQUENTIAL (|I-J|=1), 101 MEDIUM RANGE (1 < |I-J| <=5) AND 245 LONG RANGE (|I-J| >5) INTERRESIDUES AND 70 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 64 DISTANCE RESTRAINTS FOR 32 HYDROGEN BONDS; 157 TORSION ANGLE (78 PHI, 10 PSI, 55 CHI1 AND 14 CHI2) RESTRAINTS; 91 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 184 (93 CALPHA AND 91 CBETA) 13C SHIFT RESTRAINTS.

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99 - 103) AND CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) RESTRAINTS. THE COORDINATES OF THE 40 FINAL SIMULATED ANNEALING STRUCTURES ARE PRESENTED IN THIS ENTRY. THE B FACTOR FIELD PRESENTS THE AVERAGE RMS OF THE 40 INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS OBTAINED BY BEST FITTING RESIDUES 76 - 94, 97 - 102, 106 -147, 181 - 191, AND 194 -199. THESE RESIDUES CORRESPOND TO THE NON-MOBILE CORE OF THE PROTEIN AS EVIDENCED BY 15N RELAXATION DATA.
NMR ensembleConformers submitted total number: 40

+
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://pdbjlvh1.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