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- PDB-3skm: Crystal structure of the HLA-B8FLRGRAYVL, mutant G8V of the FLR p... -

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Basic information

Entry
Database: PDB / ID: 3skm
TitleCrystal structure of the HLA-B8FLRGRAYVL, mutant G8V of the FLR peptide
Components
  • Beta-2-microglobulin
  • Epstein-Barr nuclear antigen 3
  • HLA class I histocompatibility antigen, B-8 alpha chain
KeywordsIMMUNE SYSTEM / T cell receptor
Function / homology
Function and homology information


host cell nuclear matrix / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / viral process ...host cell nuclear matrix / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / viral process / detection of bacterium / secretory granule membrane / 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 / 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 / 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 / defense response / 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 / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / 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 / : ...Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / 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, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Epstein-Barr nuclear antigen 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGras, S. / Wilmann, P.G. / Zhenjun, C. / Hanim, H. / Yu Chih, L. / Kjer-Nielsen, L. / Purcell, A.W. / Burrows, S.R. / Mccluskey, J. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2012
Title: A structural basis for varied alpha-beta TCR usage against an immunodominant EBV antigen restricted to a HLA-B8 molecule.
Authors: Gras, S. / Wilmann, P.G. / Chen, Z. / Halim, H. / Liu, Y.C. / Kjer-Nielsen, L. / Purcell, A.W. / Burrows, S.R. / McCluskey, J. / Rossjohn, J.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Structure summary
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 3


Theoretical massNumber of molelcules
Total (without water)44,9043
Polymers44,9043
Non-polymers00
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-21 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 81.680, 112.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein HLA class I histocompatibility antigen, B-8 alpha chain / MHC class I antigen B*8


Mass: 31927.977 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 25-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30460, UniProt: P01889*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, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide Epstein-Barr nuclear antigen 3 / EBNA-3 / EBV nuclear antigen 3 / Epstein-Barr nuclear antigen 3A / EBNA-3A / EBV nuclear antigen 3A


Mass: 1096.326 Da / Num. of mol.: 1 / Fragment: sequence database residues 325-333 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KST2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 20% PEG 4000, 0.1M tri-Na citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 43886 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.611 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.46
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.574.855294664571100
1.9-20.357.384318952601100
2-2.10.2559.713545743201100
2.1-2.20.20311.572935635751100
2.2-2.30.16213.642426229651100
2.3-2.40.14215.012048625071100
2.4-2.50.12916.311732921201100
2.5-30.09120.585595469261100
3-3.50.06128.22790335331100
3.5-40.05132.971563420191100
4-50.04635.681534920211100
5-60.04534.3269799061100
6-100.04334.3754410161100
10-1000.03835.81748261184.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M05

1m05


Resolution: 1.8→19.885 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8756 / SU ML: 0.2 / σ(F): 0.01 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 2149 5.04 %
Rwork0.1752 --
obs0.1771 42649 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.476 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 85.48 Å2 / Biso mean: 22.4819 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.0959 Å2-0 Å20 Å2
2---2.3026 Å2-0 Å2
3---4.3985 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 0 439 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063434
X-RAY DIFFRACTIONf_angle_d1.0334686
X-RAY DIFFRACTIONf_chiral_restr0.08473
X-RAY DIFFRACTIONf_plane_restr0.004634
X-RAY DIFFRACTIONf_dihedral_angle_d13.2571297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86430.24282130.21043722393591
1.8643-1.93890.25991970.18983872406994
1.9389-2.0270.23672350.18093887412295
2.027-2.13380.18932110.17634018422997
2.1338-2.26730.23082020.1724044424698
2.2673-2.44210.21512160.17544058427498
2.4421-2.68730.23142130.18524133434699
2.6873-3.07490.24672020.18664173437599
3.0749-3.86940.19222280.166542164444100
3.8694-19.88580.17412320.15543774609100

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