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

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Basic information

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


glucan 1,4-alpha-maltotriohydrolase activity / maltose catabolic process / oligo-1,6-glucosidase activity / alpha-1,4-glucosidase activity / alpha-glucosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...glucan 1,4-alpha-maltotriohydrolase activity / maltose catabolic process / oligo-1,6-glucosidase activity / alpha-1,4-glucosidase activity / alpha-glucosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / alpha-amylase activity / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Glycosyl hydrolase, all-beta / 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 ...Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Glycosyl hydrolase, all-beta / 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 / Glycoside hydrolase superfamily / 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 / Alpha-glucosidase MAL32
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
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.
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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS I H-2KB HEAVY CHAIN
B: BETA-2 MICROGLOBULIN
P: YEAST ALPHA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)44,4423
Polymers44,4423
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-16 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.010, 89.420, 45.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 YEAST ALPHA-GLUCOSIDASE / MALTASE


Mass: 1089.208 Da / Num. of mol.: 1 / Fragment: RESIDUES 438 - 446 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38158, alpha-glucosidase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSOURCE MOLECULE_NAME: MALTASE, YEAST ALPHA-GLUCOSIDASE (RESIDUES 438 - 446). SOURCE OF PEPTIDE ...SOURCE MOLECULE_NAME: MALTASE, YEAST ALPHA-GLUCOSIDASE (RESIDUES 438 - 446). SOURCE OF PEPTIDE UNKNOWN. SEQUENCE CONFIRMED BY MAP INTERPRETATION AND AMINO TERMINAL SEQUENCING OF THE ACID EXTRACTED PEPTIDE. MOST LIKELY THE PEPTIDE IS DERIVED FROM THE DROSOPHILA CELL CULTURE MEDIA. 100% SEQUENCE HIT WITH RESIDUES 438 - 446 SP|P38158|MA3S_YEAST ALPHA-GLUCOSIDASE MAL3S (EC 3.2.1.20) (MALTASE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.4 %

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 18677 / % possible obs: 91.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.068

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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
Rwork0.16 -
obs0.16 14437
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 0 129 3257
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

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