[English] 日本語
Yorodumi
- PDB-5nui: Crystal structure of SIVmac239 Nef in an ExxxLM endocytic sorting... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nui
TitleCrystal structure of SIVmac239 Nef in an ExxxLM endocytic sorting motif bound state
Components
  • Protein Nef
  • SER-GLN-ILE-LYS-ARG-LEU-LEU-SER
KeywordsVIRAL PROTEIN / SIV / Nef / endocytic sorting motif / ExxxLL
Function / homology
Function and homology information


receptor-mediated endocytosis of virus by host cell / virus-mediated perturbation of host defense response / GTP binding
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / 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 speciesSimian immunodeficiency virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsManrique, S. / Horenkamp, F.A. / Anand, K. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGE 976/6-1 Germany
CitationJournal: Nat Commun / Year: 2017
Title: Endocytic sorting motif interactions involved in Nef-mediated downmodulation of CD4 and CD3.
Authors: Manrique, S. / Sauter, D. / Horenkamp, F.A. / Lulf, S. / Yu, H. / Hotter, D. / Anand, K. / Kirchhoff, F. / Geyer, M.
History
DepositionApr 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Nef
B: Protein Nef
M: SER-GLN-ILE-LYS-ARG-LEU-LEU-SER


Theoretical massNumber of molelcules
Total (without water)36,6713
Polymers36,6713
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.480, 140.730, 106.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Protein Nef


Mass: 17645.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Gene: nef / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QGG3
#2: Protein/peptide SER-GLN-ILE-LYS-ARG-LEU-LEU-SER


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 4000, 0.15 M ammonium sulfate, 0.1 M MES (pH 5.8)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9778 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.5→44.018 Å / Num. obs: 13775 / % possible obs: 99.9 % / Observed criterion σ(F): 2.08 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20
Reflection shellHighest resolution: 2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 794 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2685: ???)refinement
XDS(dev_2685: ???)data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IK5

3ik5


Resolution: 2.5→44.018 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 1031 7.5 %
Rwork0.1947 --
obs0.1995 13751 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 49 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072078
X-RAY DIFFRACTIONf_angle_d0.8332833
X-RAY DIFFRACTIONf_dihedral_angle_d8.1041195
X-RAY DIFFRACTIONf_chiral_restr0.047287
X-RAY DIFFRACTIONf_plane_restr0.007354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.63180.42871450.34681776X-RAY DIFFRACTION99
2.6318-2.79670.33161440.26741787X-RAY DIFFRACTION100
2.7967-3.01260.28091450.24121801X-RAY DIFFRACTION100
3.0126-3.31570.33711450.22741782X-RAY DIFFRACTION100
3.3157-3.79520.29991470.20061821X-RAY DIFFRACTION100
3.7952-4.78070.21531490.1631836X-RAY DIFFRACTION100
4.7807-44.02480.22081560.17591917X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.0387 Å / Origin y: -30.9732 Å / Origin z: 8.3209 Å
111213212223313233
T0.4064 Å2-0.0302 Å2-0.0343 Å2-0.4517 Å2-0.0915 Å2--0.3988 Å2
L0.7059 °20.4386 °2-0.6726 °2-3.2646 °2-1.9584 °2--1.5585 °2
S0.0145 Å °-0.2171 Å °0.0122 Å °0.0736 Å °-0.0822 Å °-0.1133 Å °-0.0957 Å °0.1393 Å °0.0794 Å °
Refinement TLS groupSelection details: all

+
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