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- PDB-1hhh: THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARIS... -

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Basic information

Entry
Database: PDB / ID: 1hhh
TitleTHE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2
Components
  • BETA 2-MICROGLOBULIN
  • CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN)
  • HEPATITIS B NUCLEOCAPSID PROTEIN (RESIDUES 18-27)
KeywordsHISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / 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 ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / 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 / 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 / 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 / viral penetration into host nucleus / 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 / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / host cell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / 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 / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / 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 ...Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / 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 / Capsid protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsMadden, D.R. / Garboczi, D.N. / Wiley, D.C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.
Authors: Madden, D.R. / Garboczi, D.N. / Wiley, D.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides
Authors: Garboczi, D.N. / Hung, D.T. / Wiley, D.C.
#2: Journal: J.Virol. / Year: 1993
Title: Definition of a Minimal Optimal Cytotoxic T-Cell Epitope within the Hepatitis B Virus Nucleocapsid Protein
Authors: Bertoletti, A. / Chisari, F.V. / Penna, A. / Guilhot, S. / Galati, L. / Missale, G. / Fowler, P. / Schlicht, H.-J. / Vitiello, A. / Chesnut, R.C. / Fiaccadori, F. / Ferrari, C.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#4: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution
Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C.
#5: 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.
#6: 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.
#7: 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
DepositionJun 30, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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-A*0201) (ALPHA CHAIN)
B: BETA 2-MICROGLOBULIN
C: HEPATITIS B NUCLEOCAPSID PROTEIN (RESIDUES 18-27)


Theoretical massNumber of molelcules
Total (without water)44,8893
Polymers44,8893
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-24 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.630, 81.240, 94.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO A 210 AND PRO B 32 ARE CIS PROLINES.
2: ESCHERICHIA COLI EXPRESSED BETA-2 MICROGLOBULIN CONTAINS AN N-TERMINAL METHIONINE, IDENTIFIED HERE BY RESIDUE NUMBER 0.

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Components

#1: Protein CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN)


Mass: 31854.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-2-MICROGLOBULIN / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA 2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-2-MICROGLOBULIN / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide HEPATITIS B NUCLEOCAPSID PROTEIN (RESIDUES 18-27)


Mass: 1155.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Genus: Orthohepadnavirus / References: UniProt: P12901
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*).
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 %PEG60001reservoir
225 mMn-morpholinoethanesulfanolamine1reservoir
30.1 %sodium azide1reservoir

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.286 / Rfactor obs: 0.286 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 0 3167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.7
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
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / Num. reflection obs: 7680 / Rfactor obs: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.7

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