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- PDB-2mha: CRYSTAL STRUCTURE OF THE MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I... -

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Basic information

Entry
Database: PDB / ID: 2mha
TitleCRYSTAL STRUCTURE OF THE MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I H-2KB MOLECULE CONTAINING A SINGLE VIRAL PEPTIDE: IMPLICATIONS FOR PEPTIDE BINDING AND T-CELL RECEPTOR RECOGNITION
Components
  • BETA 2-MICROGLOBULIN
  • CLASS I HISTOCOMPATIBILITY ANTIGEN (H-2KB) (ALPHA CHAIN)
  • VIRAL OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
KeywordsHISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / viral nucleocapsid / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / defense response to bacterium / ribonucleoprotein complex / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / cytosol
Similarity search - Function
Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid 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 ...Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vesicular stomatitis virus
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsZhang, W. / Young, A.C.M. / Imarai, M. / Nathenson, S.G. / Sacchettini, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal structure of the major histocompatibility complex class I H-2Kb molecule containing a single viral peptide: implications for peptide binding and T-cell receptor recognition.
Authors: Zhang, W. / Young, A.C. / Imarai, M. / Nathenson, S.G. / Sacchettini, J.C.
History
DepositionJul 21, 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 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 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: CLASS I HISTOCOMPATIBILITY ANTIGEN (H-2KB) (ALPHA CHAIN)
B: BETA 2-MICROGLOBULIN
C: CLASS I HISTOCOMPATIBILITY ANTIGEN (H-2KB) (ALPHA CHAIN)
D: BETA 2-MICROGLOBULIN
E: VIRAL OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
F: VIRAL OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU


Theoretical massNumber of molelcules
Total (without water)87,5026
Polymers87,5026
Non-polymers00
Water00
1
A: CLASS I HISTOCOMPATIBILITY ANTIGEN (H-2KB) (ALPHA CHAIN)
B: BETA 2-MICROGLOBULIN
E: VIRAL OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU


Theoretical massNumber of molelcules
Total (without water)43,7513
Polymers43,7513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-17 kcal/mol
Surface area19600 Å2
MethodPISA
2
C: CLASS I HISTOCOMPATIBILITY ANTIGEN (H-2KB) (ALPHA CHAIN)
D: BETA 2-MICROGLOBULIN
F: VIRAL OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU


Theoretical massNumber of molelcules
Total (without water)43,7513
Polymers43,7513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-16 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.900, 92.200, 67.500
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO A 210, PRO B 32, PRO C 210 AND PRO D 32 ARE CIS PROLINES.

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Components

#1: Protein CLASS I HISTOCOMPATIBILITY ANTIGEN (H-2KB) (ALPHA CHAIN)


Mass: 31090.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: unidentified (others) / References: UniProt: P01901
#2: Protein BETA 2-MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: unidentified (others) / References: UniProt: P01887
#3: Protein/peptide VIRAL OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU


Mass: 956.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis virus / Genus: Vesiculovirus / References: UniProt: P11212
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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mmagnesium acetate1reservoir
20.1 Mcacodylate1reservoir
312-15 %PEG80001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 19176 / % possible obs: 79.5 % / Observed criterion σ(I): 3.34

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→54.2 Å / Rfactor Rwork: 0.184 / Rfactor obs: 0.184
Refinement stepCycle: LAST / Resolution: 2.5→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 0 0 6160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.94
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: 2.8 Å / Num. reflection obs: 19176 / σ(I): 3.34 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.94
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_deg

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