[English] 日本語
Yorodumi
- PDB-3gsr: Crystal structure of the binary complex between HLA-A2 and HCMV N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gsr
TitleCrystal structure of the binary complex between HLA-A2 and HCMV NLV-M5V peptide variant
Components
  • Beta-2-microglobulin
  • HCMV pp65 fragment 495-503, variant M5V (NLVPVVATV)
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / HLA / HUMAN CYTOMEGALOVIRUS / PP65 / T CELL RECEPTOR (TCR) / IMMUNE RESPONSE / PUBLIC RESPONSE / IMMUNODOMINANCE / RESTRAINED RESPONSE / HOST-VIRUS INTERACTION / MEMBRANE / MHC I / POLYMORPHISM / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


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 ...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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
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 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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsReiser, J.-B. / Saulquin, X. / Gras, S. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. ...Reiser, J.-B. / Saulquin, X. / Gras, S. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / Malissen, B. / Bonneville, M. / Housset, D.
CitationJournal: J.Immunol. / Year: 2009
Title: Structural bases for the affinity-driven selection of a public TCR against a dominant human cytomegalovirus epitope.
Authors: Gras, S. / Saulquin, X. / Reiser, J.B. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / ...Authors: Gras, S. / Saulquin, X. / Reiser, J.B. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / Malissen, B. / Bonneville, M. / Housset, D.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
P: HCMV pp65 fragment 495-503, variant M5V (NLVPVVATV)


Theoretical massNumber of molelcules
Total (without water)44,5443
Polymers44,5443
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-20 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.019, 81.011, 57.667
Angle α, β, γ (deg.)90.000, 114.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31753.139 Da / Num. of mol.: 1 / Mutation: A245V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA, HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LaqQ1 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, Beta-2 microglubulin, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LaqQ1 / References: UniProt: P61769
#3: Protein/peptide HCMV pp65 fragment 495-503, variant M5V (NLVPVVATV)


Mass: 911.095 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9-20% PEG 6000, 0.1M tri-Na Citrate, 0-0.1M NaCl, pH 6.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 36050 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.304 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.65 / Net I/σ(I): 15.35
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 12493 / Num. unique all: 3011 / Num. unique obs: 3284 / Rsym value: 0.376 / % possible all: 90.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→14.91 Å / Cor.coef. Fo:Fc: 0.948 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.818 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3295 10.1 %RANDOM
Rwork0.193 ---
all0.194 36050 --
obs0.194 31902 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 58.37 Å2 / Biso mean: 29.014 Å2 / Biso min: 16.09 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 0 175 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213297
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9224497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17123.22177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35715541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6961529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022606
X-RAY DIFFRACTIONr_nbd_refined0.1880.21340
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.28
X-RAY DIFFRACTIONr_mcbond_it0.6991.52014
X-RAY DIFFRACTIONr_mcangle_it1.17723154
X-RAY DIFFRACTIONr_scbond_it1.54631514
X-RAY DIFFRACTIONr_scangle_it2.3134.51331
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 247 -
Rwork0.241 2370 -
all-2617 -
obs--99.2 %

+
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