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- PDB-3hla: HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN A2.1 -

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Basic information

Entry
Database: PDB / ID: 3hla
TitleHUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN A2.1
Components
  • BETA 2-MICROGLOBULIN
  • CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A2.1) (ALPHA CHAIN)
KeywordsHISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


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 / 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 ...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 / 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 / endoplasmic reticulum exit site / TAP binding / beta-2-microglobulin binding / 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 / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of iron ion transport / 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 / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / 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 neurogenesis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / protein refolding / ER-Phagosome pathway / early endosome membrane / 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 / Golgi membrane / external side of plasma membrane / signaling receptor binding / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / RNA binding
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
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 / Resolution: 2.6 Å
AuthorsSaper, M.A. / Bjorkman, P.J. / Wiley, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution.
Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C.
#1: Journal: Nature / Year: 1989
Title: Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68
Authors: Garrett, T.P.J. / Saper, M.A. / Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
#2: Journal: Nature / Year: 1987
Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#3: Journal: Nature / Year: 1987
Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#4: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes
Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
History
DepositionOct 6, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE ...SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS SB1, SB2 AND SD1, SD2 RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR LAST STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A2.1) (ALPHA CHAIN)
B: BETA 2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)42,9162
Polymers42,9162
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-7 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.350, 80.400, 56.490
Angle α, β, γ (deg.)90.00, 120.42, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: GLY A 1 IS POSSIBLY DISORDERED. / 2: VAL A 28 HAS A BAD TAU ANGLE. / 3: ARG A 82 MAY HAVE AN ALTERNATE SIDECHAIN CONFORMATION. / 4: THR A 94 HAS A NONPLANAR OMEGA ANGLE.
5: TYR A 116 HAS FAIR ELECTRON DENSITY NOT TYPICAL OF MOST OTHER TYROSINES IN THIS STRUCTURE.
6: PRO A 267, LYS A 268, PRO A 269, AND LEU A 270 ARE DISORDERED. THE FIT IS TENTATIVE. PRO A 267 HAS BAD GEOMETRY.
7: PROLINES A 210 AND B 32 ARE CIS PROLINES.

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Components

#1: Protein CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A2.1) (ALPHA CHAIN)


Mass: 31167.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: LYMPHOBLASTOID CELL LINE / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA 2-MICROGLOBULIN


Mass: 11748.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: LYMPHOBLASTOID CELL LINE / References: UniProt: P61769
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER (PROGRAM *DSSP*). THE FRAGMENT CRYSTALLIZED WAS THE EXTRACELLULAR PORTION OF THE PROTEIN CLEAVED FROM THE CELL MEMBRANE WITH PAPAIN.
Has protein modificationY
Nonpolymer detailsA CARBOHYDRATE MOIETY IS ATTACHED AT RESIDUE ASN A 86 BUT IT HAS NOT BEEN MODELED. THUS NO ...A CARBOHYDRATE MOIETY IS ATTACHED AT RESIDUE ASN A 86 BUT IT HAS NOT BEEN MODELED. THUS NO COORDINATES ARE PRESENT IN THIS ENTRY FOR THIS CARBOHYDRATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.32 %

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 9999 Å / % possible obs: 47 % / Num. measured all: 16679

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→6 Å / Rfactor Rwork: 0.169
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 0 46 3064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 6 Å / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 3 Å / Total num. of bins used: 10 / Num. reflection obs: 827 / Rfactor obs: 0.12

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