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- PDB-3spv: Crystal structure of a peptide-HLA complex -

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Basic information

Entry
Database: PDB / ID: 3spv
TitleCrystal structure of a peptide-HLA complex
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-8 alpha chain
  • peptide from Trans-activator protein BZLF1
KeywordsIMMUNE SYSTEM / immunology / receptor / HLA / HLA-B*0801 / EBV / MHC / TCR / T cell
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / 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 / defense response / 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 / 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 / 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 protein binding / tertiary granule lumen / DAP12 signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / adaptive immune response / sequence-specific DNA binding / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / protein dimerization activity / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / DNA-binding transcription factor activity / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / innate immune response / focal adhesion / Neutrophil degranulation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain 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
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / Lytic switch protein BZLF1 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsGras, S. / Rossjohn, J.
CitationJournal: To be Published
Title: Crystal structure of a peptide-HLA complex
Authors: Gras, S. / Rossjohn, J.
History
DepositionJul 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8236
Polymers44,6823
Non-polymers1413
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-28 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.560, 81.460, 110.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-8 alpha chain / HLA B8 heavy chain / MHC class I antigen B*8


Mass: 31927.977 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / 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: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide peptide from Trans-activator protein BZLF1 / EB1 / Zebra


Mass: 1006.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: P03206

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Non-polymers , 3 types, 539 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 15-20% PEG 4000, 0.2M ammonium acetate, 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 315r / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 111282 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 16.952 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.3-1.40.3310.4544.3617521822099216880.48598.1
1.4-1.50.2060.2996.5113299116629164180.31998.7
1.5-20.0860.12713.7833528742100418360.13699.4
2-2.50.0370.0724.9611500715113150860.07599.8
2.5-30.0270.05629.0352766675367530.06100
3-40.0220.04732.1641774542954270.05100
4-50.0180.0433.2215118197419650.04399.5
5-60.0170.03732.4767838818770.03999.5
6-100.0170.03532.0273919959920.03899.7
100.0160.03330.4815653012400.03679.7

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m05

1m05


Resolution: 1.3→19.584 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8615 / SU ML: 0.17 / σ(F): 0.01 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 5202 5.02 %
Rwork0.1959 --
obs0.1971 103679 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.52 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 72.32 Å2 / Biso mean: 15.5851 Å2 / Biso min: 4.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.3902 Å2-0 Å20 Å2
2---1.7308 Å2-0 Å2
3---1.3406 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 9 536 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063648
X-RAY DIFFRACTIONf_angle_d1.0365009
X-RAY DIFFRACTIONf_chiral_restr0.073504
X-RAY DIFFRACTIONf_plane_restr0.005687
X-RAY DIFFRACTIONf_dihedral_angle_d12.361384
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 (%)
1.2999-1.34630.32644620.2888481894381
1.3463-1.40020.29174800.26398722920283
1.4002-1.46390.26694750.24089164963987
1.4639-1.54110.25175230.211495381006190
1.5411-1.63760.22625010.196698771037893
1.6376-1.7640.21675360.186100271056395
1.764-1.94130.20285490.1896103511090097
1.9413-2.22190.19175640.184105081107299
2.2219-2.79810.22965450.1912107431128899
2.7981-19.58650.19375670.17741106611633100

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