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- PDB-3ft3: Crystal Structure of the minor histocompatibility peptide HA-1His... -

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Basic information

Entry
Database: PDB / ID: 3ft3
TitleCrystal Structure of the minor histocompatibility peptide HA-1His in complex with HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • histidine variant HA-1 peptide
KeywordsIMMUNE SYSTEM / HLA / HUMAN MINOR H ANTIGENS / ANTIGEN PROCESSING / ANTIGEN PRESENTATION / IMMUNE RESPONSE / IMMUNOGENICITY / MEMBRANE / MHC I / POLYMORPHISM / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / GRAFT REJECTION / HOST-VERSUS-GRAFT DISEASE / GRAFT-VERSUS-TUMOR IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of small GTPase mediated signal transduction / regulation of small GTPase mediated signal transduction / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding ...negative regulation of small GTPase mediated signal transduction / regulation of small GTPase mediated signal transduction / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / CDC42 GTPase cycle / TAP binding / endoplasmic reticulum exit site / RHOA GTPase cycle / detection of bacterium / 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 / beta-2-microglobulin binding / T cell receptor binding / RAC1 GTPase cycle / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of T cell mediated cytotoxicity / DAP12 interactions / Endosomal/Vacuolar pathway / GTPase activator activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / positive regulation of type II interferon production / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / T cell receptor signaling pathway / ruffle membrane / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / azurophil granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / E3 ubiquitin ligases ubiquitinate target proteins / ER-Phagosome pathway / early endosome membrane / secretory granule lumen / antibacterial humoral response / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / signal transduction
Similarity search - Function
: / Rho GTPase-activating protein 29/45 N-terminal / : / : / GEM-interacting protein-like, FCH domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily ...: / Rho GTPase-activating protein 29/45 N-terminal / : / : / GEM-interacting protein-like, FCH domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Rho GTPase-activating protein 45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsReiser, J.-B. / Gras, S. / Chouquet, A. / Le Gorrec, M. / Spierings, E. / Goulmy, E. / Housset, D.
CitationJournal: J.Immunol. / Year: 2009
Title: Steric hindrance and fast dissociation explain the lack of immunogenicity of the minor histocompatibility HA-1Arg Null allele.
Authors: Spierings, E. / Gras, S. / Reiser, J.B. / Mommaas, B. / Almekinders, M. / Kester, M.G. / Chouquet, A. / Le Gorrec, M. / Drijfhout, J.W. / Ossendorp, F. / Housset, D. / Goulmy, E.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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, A-2 alpha chain
B: Beta-2-microglobulin
P: histidine variant HA-1 peptide


Theoretical massNumber of molelcules
Total (without water)44,7873
Polymers44,7873
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-20 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.470, 79.750, 54.210
Angle α, β, γ (deg.)90.00, 111.02, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asymmetric unit.

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31882.254 Da / Num. of mol.: 1 / Mutation: A269V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA, HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90F LaqQ1 / References: UniProt: P01892, UniProt: P04439*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, beta-2 microglubuline, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90F LaqQ1 / References: UniProt: P61769
#3: Protein/peptide histidine variant HA-1 peptide


Mass: 1025.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide / References: UniProt: Q92619*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12-15% w/v PEG 6000, 0.1 M NaCl and 0.1 M tri-sodium-citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 29304 / Num. obs: 29304 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.109 / Net I/σ(I): 10.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2824 / Rsym value: 0.461 / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.952 / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23054 2934 -random
Rwork0.18191 ---
all0.18406 29299 --
obs0.18406 29299 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.857 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0.85 Å2
2---1.75 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 0 155 3488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213450
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9224717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81223.189185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5615564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2761530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022781
X-RAY DIFFRACTIONr_nbd_refined0.2250.31523
X-RAY DIFFRACTIONr_nbtor_refined0.3140.52355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.5367
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.521
X-RAY DIFFRACTIONr_mcbond_it0.8822044
X-RAY DIFFRACTIONr_mcangle_it1.52133328
X-RAY DIFFRACTIONr_scbond_it1.39731406
X-RAY DIFFRACTIONr_scangle_it2.03241389
LS refinement shellResolution: 1.95→2.017 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.318 266 -
Rwork0.246 2734 -
obs-2734 94.93 %

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