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- PDB-1i7r: CRYSTAL STRUCTURE OF CLASS I MHC A2 IN COMPLEX WITH PEPTIDE P1058 -

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Basic information

Entry
Database: PDB / ID: 1i7r
TitleCRYSTAL STRUCTURE OF CLASS I MHC A2 IN COMPLEX WITH PEPTIDE P1058
Components
  • 9 RESIDUE PEPTIDE
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
KeywordsIMMUNE SYSTEM / MHC fold
Function / homology
Function and homology information


: / : / retina homeostasis / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...: / : / retina homeostasis / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation
Similarity search - Function
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 ...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
Beta-2-microglobulin / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBusslep, J. / Zhao, R. / Loftus, D. / Appella, E. / Collins, E.J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: T cell activity correlates with oligomeric peptide/MHC binding on T cell surface
Authors: Busslep, J. / Zhao, R. / Donnini, D. / Loftus, D. / Saad, M. / Appella, E. / Collins, E.J.
History
DepositionMar 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: 9 RESIDUE PEPTIDE
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: 9 RESIDUE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)89,5846
Polymers89,5846
Non-polymers00
Water1,910106
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: 9 RESIDUE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,7923
Polymers44,7923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-22 kcal/mol
Surface area19490 Å2
MethodPISA
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: 9 RESIDUE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,7923
Polymers44,7923
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-22 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.860, 63.820, 75.870
Angle α, β, γ (deg.)82.09, 76.20, 78.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLAA / Plasmid: PLM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / 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: PLM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01884, UniProt: P61769*PLUS
#3: Protein/peptide 9 RESIDUE PEPTIDE


Mass: 1058.227 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The nine residue peptide was chemically synthesized
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 1998
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0789 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 44322 / Num. obs: 44322 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.232 / % possible all: 93.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 2252 -random
Rwork0.264 ---
all0.266 45809 --
obs0.266 44322 96.7 %-
Displacement parametersBiso mean: 19.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 0 106 6428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d2.169

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