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- PDB-3vfo: crystal structure of HLA B*3508 LPEP157A, HLA mutant Ala157 -

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Basic information

Entry
Database: PDB / ID: 3vfo
Titlecrystal structure of HLA B*3508 LPEP157A, HLA mutant Ala157
Components
  • Beta-2-microglobulin
  • LPEP peptide from EBV, LPEPLPQGQLTAY
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA B*3508 / Epstein Barr virus / TCR / T cell / antigen-presenting molecule
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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of ferrous iron binding / positive regulation of transferrin 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 ...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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / sequence-specific DNA binding / amyloid fibril formation / learning or memory / protein dimerization activity / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / signaling receptor binding / focal adhesion / virus-mediated perturbation of host defense response / Neutrophil degranulation / regulation of DNA-templated transcription / host cell nucleus / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA-B*3507 / Lytic switch protein BZLF1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsLiu, Y.C. / Rossjohn, J. / Gras, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Energetic Basis Underpinning T-cell Receptor Recognition of a Super-bulged Peptide Bound to a Major Histocompatibility Complex Class I Molecule.
Authors: Liu, Y.C. / Chen, Z. / Burrows, S.R. / Purcell, A.W. / McCluskey, J. / Rossjohn, J. / Gras, S.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
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 1.3Oct 30, 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: MHC class I antigen
B: Beta-2-microglobulin
C: LPEP peptide from EBV, LPEPLPQGQLTAY


Theoretical massNumber of molelcules
Total (without water)45,0733
Polymers45,0733
Non-polymers00
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-21 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 81.520, 110.980
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 MHC class I antigen


Mass: 31898.168 Da / Num. of mol.: 1 / Mutation: R157A
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: C5MK56
#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 LPEP peptide from EBV, LPEPLPQGQLTAY


Mass: 1426.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BL biochem / References: UniProt: P03206*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 16% PEG 4K, 0.1M sodium citrate pH5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionNumber: 307782 / Rmerge(I) obs: 0.058 / D res high: 1.7 Å / Num. obs: 47342 / % possible obs: 91.6
Diffraction reflection shellHighest resolution: 1.7 Å / Lowest resolution: 1.8 Å / Num. obs: 7925 / % possible obs: 99.4 % / Rmerge(I) obs: 0.252
ReflectionHighest resolution: 1.7 Å / Num. obs: 47342 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.87 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.32
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5.58 / Num. measured obs: 47321 / Num. unique obs: 7925 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZHK

1zhk


Resolution: 1.7→19.413 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8222 / SU ML: 0.59 / σ(F): 1.34 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2788 2387 5.08 %
Rwork0.2459 --
obs0.2476 46986 91.02 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.134 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 62.34 Å2 / Biso mean: 17.8423 Å2 / Biso min: 3.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.6982 Å2-0 Å20 Å2
2---1.9848 Å2-0 Å2
3---3.683 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 0 471 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073322
X-RAY DIFFRACTIONf_angle_d1.0474520
X-RAY DIFFRACTIONf_chiral_restr0.074460
X-RAY DIFFRACTIONf_plane_restr0.004603
X-RAY DIFFRACTIONf_dihedral_angle_d14.7981241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6999-1.73460.30921330.26292769290298
1.7346-1.77230.25551690.238228543023100
1.7723-1.81350.28261610.227428463007100
1.8135-1.85880.27891710.249927832954100
1.8588-1.9090.6377870.48691678176559
1.909-1.96520.5712660.50881652171857
1.9652-2.02850.28651500.23922781293198
2.0285-2.1010.25681420.202528873029100
2.101-2.1850.24381440.228528442988100
2.185-2.28430.6196740.53071525159953
2.2843-2.40450.27741340.24722624275891
2.4045-2.55480.23741830.205228543037100
2.5548-2.75160.25271690.213928543023100
2.7516-3.02750.27761500.216529183068100
3.0275-3.46350.2331570.20729103067100
3.4635-4.35550.23881280.20622741286992
4.3555-19.41470.2141690.19330793248100

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