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- PDB-1vac: MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN... -

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Basic information

Entry
Database: PDB / ID: 1vac
TitleMHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND CHICKEN OVALBUMIN
Components
  • BETA-2 MICROGLOBULIN
  • CHICKEN OVALBUMIN
  • MHC CLASS I H-2KB HEAVY CHAIN
KeywordsCOMPLEX (MHC I/PEPTIDE) / HISTOCOMPATIBILITY ANTIGEN / CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX / MHC I / COMPLEX (MHC I-PEPTIDE) COMPLEX
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / response to steroid hormone ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / response to steroid hormone / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to corticosterone / 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 / phagocytic vesicle / monoatomic ion transport / Neutrophil degranulation / response to progesterone / early endosome lumen / 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 / response to estrogen / 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 / protease binding / protein homotetramerization / vesicle / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / MHC class I, alpha chain, C-terminal ...Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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
Ovalbumin / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFremont, D.H. / Wilson, I.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.
Authors: Fremont, D.H. / Stura, E.A. / Matsumura, M. / Peterson, P.A. / Wilson, I.A.
#1: Journal: Science / Year: 1992
Title: Crystal Structures of Two Viral Peptides in Complex with Murine Mhc Class I H-2Kb
Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A.
#2: Journal: Science / Year: 1992
Title: Emerging Principles for the Recognition of Peptide Antigens by Mhc Class I Molecules
Authors: Matsumura, M. / Fremont, D.H. / Peterson, P.A. / Wilson, I.A.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of Murine Major Histocompatibility Complex Class I H-2Kb with Single Peptides
Authors: Stura, E.A. / Matsumura, M. / Fremont, D.H. / Saito, Y. / Peterson, P.A. / Wilson, I.A.
History
DepositionNov 1, 1994Processing site: BNL
Revision 1.0Jun 20, 1996Provider: 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC CLASS I H-2KB HEAVY CHAIN
B: BETA-2 MICROGLOBULIN
P: CHICKEN OVALBUMIN


Theoretical massNumber of molelcules
Total (without water)44,3173
Polymers44,3173
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-22 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.000, 60.900, 83.800
Angle α, β, γ (deg.)90.00, 107.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC CLASS I H-2KB HEAVY CHAIN


Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/B / Gene: BETA-2-MICROGLOBULIN / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901
#2: Protein BETA-2 MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/B / Gene: BETA-2-MICROGLOBULIN / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887
#3: Protein/peptide CHICKEN OVALBUMIN


Mass: 964.137 Da / Num. of mol.: 1 / Fragment: RESIDUES 257 - 264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P01012
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 3.24 Å3/Da / Density % sol: 62 %
Crystal
*PLUS
Density % sol: 62 %
Crystal grow
*PLUS
Temperature: 17.0 ℃ / pH: 6.2 / Method: unknown / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Msodium potassium phosphate11
21 %MPD11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 18598 / % possible obs: 93.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 43371

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Processing

Software
NameVersionClassification
XENGENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.173 -
obs0.173 14952
Displacement parametersBiso mean: 35.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 0 109 3230
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.9
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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