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- PDB-4prn: Crystal structure of a HLA-B*35:01-HPVG-A4 -

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Basic information

Entry
Database: PDB / ID: 4prn
TitleCrystal structure of a HLA-B*35:01-HPVG-A4
Components
  • Beta-2-microglobulin
  • Epstein-Barr nuclear antigen 1
  • HLA class I histocompatibility antigen, B-35 alpha chain
KeywordsIMMUNE SYSTEM / human leukocyte antigen class I / Epstein-Barr virus / viral escape / T cell receptor / viral immunity
Function / homology
Function and homology information


viral latency / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of T cell anergy / regulation of interleukin-6 production / regulation of DNA replication / 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 ...viral latency / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of T cell anergy / regulation of interleukin-6 production / regulation of DNA replication / 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 / 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 / endonuclease activity / protein homotetramerization / adaptive immune response / symbiont-mediated suppression of host NF-kappaB cascade / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / DNA-binding transcription factor activity / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / DNA binding / extracellular exosome / extracellular region / identical protein binding / membrane
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Epstein-barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsYu Chih, L. / Rossjohn, J. / Gras, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism.
Authors: Liu, Y.C. / Chen, Z. / Neller, M.A. / Miles, J.J. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Gras, S.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Jul 2, 2014Group: Database references
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 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-35 alpha chain
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0894
Polymers45,0303
Non-polymers591
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-22 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.640, 81.230, 109.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide Epstein-Barr nuclear antigen 1 / EBNA-1 / EBV nuclear antigen 1


Mass: 1341.400 Da / Num. of mol.: 1 / Fragment: unp residues 407-417 / Source method: obtained synthetically / Source: (synth.) Epstein-barr virus (Epstein-Barr virus) / References: UniProt: Q1HVF7
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 16% PEG 4000, 0.2M ammonium acetate and 0.1M Na-Citrate pH 5.6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 55695 / Num. obs: 55695 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.29 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.035 / Net I/σ(I): 20.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.750.4054.53613128882100
1.75-1.80.3066.26275373733100
1.8-1.90.2198.58466956336100
1.9-20.14313379645155100
2-2.50.08521.1111151015185100
2.5-30.05332.08491856799100
3-50.03444.48518797426100
5-60.02847.276141888100
6-100.02547.046693997100
100.02545.83166329497.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.14data extraction
Blu-Iceicedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FYY

2fyy


Resolution: 1.65→33.192 Å / FOM work R set: 0.862 / SU ML: 0.42 / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 2820 5.06 %randomn
Rwork0.1844 ---
obs0.1863 55688 97.96 %-
all-55688 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.946 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 68.02 Å2 / Biso mean: 21.36 Å2 / Biso min: 1.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.4718 Å20 Å2-0 Å2
2---3.2804 Å20 Å2
3---5.7523 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 4 513 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123378
X-RAY DIFFRACTIONf_angle_d1.2344604
X-RAY DIFFRACTIONf_chiral_restr0.087468
X-RAY DIFFRACTIONf_plane_restr0.005616
X-RAY DIFFRACTIONf_dihedral_angle_d13.8811259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6307-1.65880.3066860.26211542162859
1.6588-1.6890.28831430.243126632806100
1.689-1.72150.27851290.230726402769100
1.7215-1.75660.25331240.215226932817100
1.7566-1.79480.23111420.202726942836100
1.7948-1.83650.2551300.19826652795100
1.8365-1.88250.23491500.193626912841100
1.8825-1.93340.22871460.18426492795100
1.9334-1.99020.23181440.190926422786100
1.9902-2.05450.21171330.186426912824100
2.0545-2.12790.22771610.187627012862100
2.1279-2.21310.22861480.179726542802100
2.2131-2.31380.19961450.177527102855100
2.3138-2.43570.22241420.187526792821100
2.4357-2.58830.21891620.192726832845100
2.5883-2.7880.23711560.1927032859100
2.788-3.06840.23381340.187527312865100
3.0684-3.5120.22271410.180727442885100
3.512-4.42310.19681490.153727802929100
4.4231-33.19890.19821550.180729133068100

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