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- PDB-1i7t: CRYSTAL STRUCTURE OF CLASS I MHC A2 IN COMPLEX WITH PEPTIDE P1049-5V -

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Basic information

Entry
Database: PDB / ID: 1i7t
TitleCRYSTAL STRUCTURE OF CLASS I MHC A2 IN COMPLEX WITH PEPTIDE P1049-5V
Components
  • 9 RESIDUE PEPTIDE
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
KeywordsIMMUNE SYSTEM / MHC fold
Function / homology
Function and homology information


: / : / : / : / : / regulation of membrane depolarization / retina homeostasis / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding ...: / : / : / : / : / regulation of membrane depolarization / retina homeostasis / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / positive regulation of protein binding / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / cellular response to lipopolysaccharide / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane
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 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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-major histocompatibility complex 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
Revision 1.3Jul 21, 2021Group: Database references / Refinement description / Category: refine / struct_ref_seq_dif
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)89,4706
Polymers89,4706
Non-polymers00
Water00
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)44,7353
Polymers44,7353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-22 kcal/mol
Surface area18370 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)44,7353
Polymers44,7353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-21 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.920, 62.930, 74.700
Angle α, β, γ (deg.)82.02, 76.28, 77.96
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


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: 1001.220 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The nine residue peptide was chemically synthesized
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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG60001reservoir
225 mMMES1reservoir
310 mg/mlprotein1drop
425 mMMES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 20521 / Num. obs: 20521 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 60.2 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 7
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 9 / Rsym value: 0.379 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96.3 %
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2021 -random
Rwork0.229 ---
obs0.23 20521 97 %-
all-21151 --
Displacement parametersBiso mean: 13.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 0 0 6312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d1.34
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.23 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.3 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 1.34

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