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- PDB-3bvn: High resolution crystal structure of HLA-B*1402 in complex with t... -

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Basic information

Entry
Database: PDB / ID: 3bvn
TitleHigh resolution crystal structure of HLA-B*1402 in complex with the latent membrane protein 2 peptide (LMP2) of Epstein-Barr virus
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B*1402 alpha chain
  • Latent membrane protein 2 peptide
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / HLA-B14 / HLA-B*14 / HLA-B1402 / HLA-B*1402 / pLMP2 / Ankylosing Spondylitis / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted / Alternative splicing / Cytoplasm / Host-virus interaction / Membrane / Phosphoprotein / Transmembrane / Ubl conjugation
Function / homology
Function and homology information


host cell endomembrane system / viral latency / : / : / 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 ...host cell endomembrane system / viral latency / : / : / 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 / 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 receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / host cell perinuclear region of cytoplasm / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Gammaherpesvirus latent membrane protein 2 / Gammaherpesvirus latent membrane protein (LMP2) protein / 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 ...Gammaherpesvirus latent membrane protein 2 / Gammaherpesvirus latent membrane protein (LMP2) protein / 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
Latent membrane protein 2 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKumar, P. / Vahedi-Faridi, A. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens
Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Merino, E. / Lopez de Castro, J.A. / Uchanska-Ziegler, B. / Ziegler, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, purification and preliminary X-ray crystallographic analysis of the human major histocompatibility antigen HLA-B*1402 in complex with a viral peptide and with a self-peptide
Authors: Kumar, P. / Vahedi-Faridi, A. / Merino, E. / Lopez de Castro, J.A. / Volz, A. / Ziegler, A. / Saenger, W. / Uchanska-Ziegler, B.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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*1402 alpha chain
B: Beta-2-microglobulin
C: Latent membrane protein 2 peptide
D: HLA class I histocompatibility antigen, B*1402 alpha chain
E: Beta-2-microglobulin
F: Latent membrane protein 2 peptide


Theoretical massNumber of molelcules
Total (without water)90,7116
Polymers90,7116
Non-polymers00
Water4,522251
1
A: HLA class I histocompatibility antigen, B*1402 alpha chain
B: Beta-2-microglobulin
C: Latent membrane protein 2 peptide


Theoretical massNumber of molelcules
Total (without water)45,3553
Polymers45,3553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, B*1402 alpha chain
E: Beta-2-microglobulin
F: Latent membrane protein 2 peptide


Theoretical massNumber of molelcules
Total (without water)45,3553
Polymers45,3553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.383, 79.953, 105.440
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B*1402 alpha chain


Mass: 32172.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pHN / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q56H30
#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 / Plasmid: pHN / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide Latent membrane protein 2 peptide


Mass: 1303.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide pLMP2 chemically synthesized / References: UniProt: P13285
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-22%(w/v) PEG 20 000, 0.1 M HEPES buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2007 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 26731 / Num. obs: 26731 / % possible obs: 93.15 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Biso Wilson estimate: 48.11 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.87
Reflection shellResolution: 2.55→2.64 Å / % possible all: 76.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UXW

1uxw


Resolution: 2.55→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1198 -RANDOM
Rwork0.2402 ---
all0.265 26731 --
obs0.2402 24383 80.8 %-
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 0 251 6615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009993
X-RAY DIFFRACTIONc_angle_deg1.63049

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