[English] 日本語
Yorodumi
- PDB-5xov: Crystal structure of peptide-HLA-A24 bound to S19-2 V-delta/V-beta TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xov
TitleCrystal structure of peptide-HLA-A24 bound to S19-2 V-delta/V-beta TCR
Components
  • Beta-2-microglobulin
  • HIV-1 Nef138-10 peptide
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • V-beta chain of T cell receptor
  • V-delta chain of T cell receptor
KeywordsIMMUNE SYSTEM / antigen presentation
Function / homology
Function and homology information


activation of transmembrane receptor protein tyrosine kinase activity / 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 / symbiont-mediated suppression of host autophagy / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...activation of transmembrane receptor protein tyrosine kinase activity / 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 / symbiont-mediated suppression of host autophagy / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / host cell Golgi membrane / 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 / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / virion component / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / SH3 domain binding / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding
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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein Nef / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.684 Å
AuthorsShi, Y. / Qi, J. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2017
Title: Conserved V delta 1 Binding Geometry in a Setting of Locus-Disparate pHLA Recognition by delta / alpha beta T Cell Receptors (TCRs): Insight into Recognition of HIV Peptides by TCRs.
Authors: Shi, Y. / Kawana-Tachikawa, A. / Gao, F. / Qi, J. / Liu, C. / Gao, J. / Cheng, H. / Ueno, T. / Iwamoto, A. / Gao, G.F.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Nov 22, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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: HIV-1 Nef138-10 peptide
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: HIV-1 Nef138-10 peptide
I: V-delta chain of T cell receptor
J: V-beta chain of T cell receptor
G: V-delta chain of T cell receptor
H: V-beta chain of T cell receptor


Theoretical massNumber of molelcules
Total (without water)190,49710
Polymers190,49710
Non-polymers00
Water7,134396
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: HIV-1 Nef138-10 peptide
I: V-delta chain of T cell receptor
J: V-beta chain of T cell receptor


Theoretical massNumber of molelcules
Total (without water)95,2485
Polymers95,2485
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-62 kcal/mol
Surface area38320 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: HIV-1 Nef138-10 peptide
G: V-delta chain of T cell receptor
H: V-beta chain of T cell receptor


Theoretical massNumber of molelcules
Total (without water)95,2485
Polymers95,2485
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-61 kcal/mol
Surface area38280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.992, 73.789, 163.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 4 types, 8 molecules ADBEIGJH

#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 A24


Mass: 31551.889 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 / Fragment: UNP residues 21-119
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
#4: Protein V-delta chain of T cell receptor


Mass: 23225.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein V-beta chain of T cell receptor


Mass: 27301.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Protein/peptide / Non-polymers , 2 types, 398 molecules CF

#3: Protein/peptide HIV-1 Nef138-10 peptide


Mass: 1290.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03407*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5%(v/v) Tacsimate pH 7.0, 0.1M HEPES, pH 7.3, 10%(w/v) polyethylene glycol monomethyl either 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 10, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 68358 / % possible obs: 99.8 % / Redundancy: 3.4 % / Net I/σ(I): 12.8
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A9E, 2IAL

1a9e

2ial


Resolution: 2.684→37.999 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.245 3459 5.06 %
Rwork0.2029 --
obs0.205 68316 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 30.36 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4395 Å20 Å20.6245 Å2
2--2.1425 Å2-0 Å2
3---1.297 Å2
Refinement stepCycle: LAST / Resolution: 2.684→37.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13416 0 0 396 13812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513792
X-RAY DIFFRACTIONf_angle_d0.87918706
X-RAY DIFFRACTIONf_dihedral_angle_d18.6024938
X-RAY DIFFRACTIONf_chiral_restr0.061968
X-RAY DIFFRACTIONf_plane_restr0.0042434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.684-2.72080.34951320.2782535X-RAY DIFFRACTION98
2.7208-2.75960.32241280.28962598X-RAY DIFFRACTION100
2.7596-2.80080.35411390.26972549X-RAY DIFFRACTION100
2.8008-2.84460.31471370.25992588X-RAY DIFFRACTION100
2.8446-2.89120.28341220.25892560X-RAY DIFFRACTION100
2.8912-2.9410.34181400.2672631X-RAY DIFFRACTION100
2.941-2.99450.32961480.24462564X-RAY DIFFRACTION100
2.9945-3.05210.25761310.23642573X-RAY DIFFRACTION100
3.0521-3.11430.2981400.23762586X-RAY DIFFRACTION100
3.1143-3.1820.25241430.23592566X-RAY DIFFRACTION100
3.182-3.2560.29131180.23182587X-RAY DIFFRACTION100
3.256-3.33740.31841520.22672612X-RAY DIFFRACTION100
3.3374-3.42760.26311470.2172573X-RAY DIFFRACTION100
3.4276-3.52830.2911340.22662601X-RAY DIFFRACTION100
3.5283-3.64210.2961290.21452579X-RAY DIFFRACTION100
3.6421-3.77220.22531290.21052616X-RAY DIFFRACTION100
3.7722-3.92310.23791450.18562610X-RAY DIFFRACTION100
3.9231-4.10140.2261240.17952601X-RAY DIFFRACTION100
4.1014-4.31740.18121310.15882608X-RAY DIFFRACTION100
4.3174-4.58750.16281360.13852637X-RAY DIFFRACTION100
4.5875-4.9410.2061580.14032570X-RAY DIFFRACTION100
4.941-5.43690.1551730.14462591X-RAY DIFFRACTION100
5.4369-6.22070.22571480.1672617X-RAY DIFFRACTION100
6.2207-7.82610.21151490.19242642X-RAY DIFFRACTION100
7.8261-38.00230.25451260.19152663X-RAY DIFFRACTION97

+
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