[English] 日本語
Yorodumi
- PDB-5hgd: HLA*A2402 complexed with HIV nef138 Y2F mutant 10mer epitope -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hgd
TitleHLA*A2402 complexed with HIV nef138 Y2F mutant 10mer epitope
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • Protein Nef
KeywordsIMMUNE SYSTEM / HLA / Antigen presentation / HIV
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / 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 / suppression by virus of host autophagy / Nef and signal transduction / Nef Mediated CD4 Down-regulation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target ...Nef mediated downregulation of CD28 cell surface expression / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / 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 / suppression by virus of host autophagy / Nef and signal transduction / Nef Mediated CD4 Down-regulation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Uncoating of the HIV Virion / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / Binding and entry of HIV virion / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / virion component / cellular response to iron(III) ion / Assembly Of The HIV Virion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / Budding and maturation of HIV virion / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / SH3 domain binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Protein Nef / HLA class I histocompatibility antigen, A alpha chain / Protein Nef / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsShi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Cell Rep / Year: 2016
Title: Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation.
Authors: Sun, X. / Shi, Y. / Akahoshi, T. / Fujiwara, M. / Gatanaga, H. / Schonbach, C. / Kuse, N. / Appay, V. / Gao, G.F. / Oka, S. / Takiguchi, M.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: Protein Nef
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: Protein Nef


Theoretical massNumber of molelcules
Total (without water)89,6746
Polymers89,6746
Non-polymers00
Water13,709761
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,8373
Polymers44,8373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-25 kcal/mol
Surface area19320 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,8373
Polymers44,8373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-24 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.655, 65.741, 87.519
Angle α, β, γ (deg.)67.97, 89.80, 89.89
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein HLA class I histocompatibility antigen, A-24 alpha chain / Aw-24 / HLA class I histocompatibility antigen / A-9 alpha chain / MHC class I antigen A*24


Mass: 31683.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#3: Protein/peptide Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 1274.511 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 135-144 / Mutation: Y2F / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P18801, UniProt: P04601*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 63675 / % possible obs: 89.9 % / Redundancy: 2.8 % / Net I/σ(I): 20.923
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 7.358 / % possible all: 91.9

-
Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.07→20.094 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 3092 5.05 %
Rwork0.1839 --
obs0.1859 61282 86.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.018 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7378 Å20.9989 Å2-3.4933 Å2
2--5.5947 Å20.7874 Å2
3----2.8569 Å2
Refinement stepCycle: LAST / Resolution: 2.07→20.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 0 761 7059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046480
X-RAY DIFFRACTIONf_angle_d0.8438772
X-RAY DIFFRACTIONf_dihedral_angle_d18.752350
X-RAY DIFFRACTIONf_chiral_restr0.061886
X-RAY DIFFRACTIONf_plane_restr0.0031154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.03020.23571290.1942545X-RAY DIFFRACTION81
2.0302-2.06350.24571440.19842460X-RAY DIFFRACTION82
2.0635-2.0990.27281240.20892613X-RAY DIFFRACTION86
2.099-2.13720.23971680.18872630X-RAY DIFFRACTION87
2.1372-2.17820.23221430.17812663X-RAY DIFFRACTION87
2.1782-2.22260.25561250.20112510X-RAY DIFFRACTION83
2.2226-2.27090.2855580.24211050X-RAY DIFFRACTION34
2.2709-2.32360.22671300.19762546X-RAY DIFFRACTION82
2.3236-2.38170.21811360.19692708X-RAY DIFFRACTION90
2.3817-2.4460.27571650.19552783X-RAY DIFFRACTION90
2.446-2.51780.26821300.19122815X-RAY DIFFRACTION91
2.5178-2.59890.25251600.19832765X-RAY DIFFRACTION92
2.5989-2.69160.25121490.18942850X-RAY DIFFRACTION93
2.6916-2.79910.28741680.18732871X-RAY DIFFRACTION93
2.7991-2.92610.23161660.18922814X-RAY DIFFRACTION94
2.9261-3.07990.25921180.1922939X-RAY DIFFRACTION95
3.0799-3.27210.2161470.17922983X-RAY DIFFRACTION96
3.2721-3.52350.23881510.1782866X-RAY DIFFRACTION94
3.5235-3.87570.16741290.16342150X-RAY DIFFRACTION71
3.8757-4.43130.16051410.14772726X-RAY DIFFRACTION90
4.4313-5.56330.18651650.15343010X-RAY DIFFRACTION98
5.5633-20.09460.19781460.18122893X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -24.9916 Å / Origin y: -15.7381 Å / Origin z: -40.6074 Å
111213212223313233
T0.1501 Å2-0.0085 Å20.0062 Å2-0.1619 Å2-0.0005 Å2--0.1618 Å2
L0.0635 °2-0.069 °20.0423 °2-0.1081 °2-0.0339 °2--0.086 °2
S0.0033 Å °0.0088 Å °0.0031 Å °-0.0044 Å °-0.0044 Å °-0.0014 Å °0.0077 Å °0.0056 Å °-0 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://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