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- PDB-1bqh: MURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8 -

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Basic information

Entry
Database: PDB / ID: 1bqh
TitleMURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8
Components
  • PROTEIN (BETA-2-MICROGLOBULIN )
  • PROTEIN (CD8A OR LYT2 OR LYT-2)
  • PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
  • PROTEIN (VSV8)
KeywordsIMMUNE SYSTEM / T-CELL / CORECEPTOR / GLYCOPROTEIN / COMPLEX / IMMUNOLOGY / ANTIGEN
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / 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 / positive regulation of natural killer cell proliferation / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of immunoglobulin production / Golgi medial cisterna / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / plasma membrane raft / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / positive regulation of interleukin-4 production / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / MHC class I protein binding / endoplasmic reticulum exit site / TAP binding / cellular defense response / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / positive regulation of calcium-mediated signaling / negative regulation of T cell proliferation / detection of bacterium / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / 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 / T cell activation / calcium-mediated signaling / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of type II interferon production / positive regulation of immune response / positive regulation of T cell activation / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / iron ion transport / protein-folding chaperone binding / antibacterial humoral response
Similarity search - Function
CD8 alpha subunit / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...CD8 alpha subunit / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, J.H. / Reinherz, E.L. / Kern, P.S. / Chang, H.C.
CitationJournal: Immunity / Year: 1998
Title: Structural basis of CD8 coreceptor function revealed by crystallographic analysis of a murine CD8alphaalpha ectodomain fragment in complex with H-2Kb.
Authors: Kern, P.S. / Teng, M.K. / Smolyar, A. / Liu, J.H. / Liu, J. / Hussey, R.E. / Spoerl, R. / Chang, H.C. / Reinherz, E.L. / Wang, J.H.
History
DepositionAug 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (BETA-2-MICROGLOBULIN )
C: PROTEIN (VSV8)
D: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
E: PROTEIN (BETA-2-MICROGLOBULIN )
F: PROTEIN (VSV8)
G: PROTEIN (CD8A OR LYT2 OR LYT-2)
H: PROTEIN (CD8A OR LYT2 OR LYT-2)
I: PROTEIN (CD8A OR LYT2 OR LYT-2)
K: PROTEIN (CD8A OR LYT2 OR LYT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,55314
Polymers146,66810
Non-polymers8854
Water0
1
A: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (BETA-2-MICROGLOBULIN )
C: PROTEIN (VSV8)
G: PROTEIN (CD8A OR LYT2 OR LYT-2)
H: PROTEIN (CD8A OR LYT2 OR LYT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7767
Polymers73,3345
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
E: PROTEIN (BETA-2-MICROGLOBULIN )
F: PROTEIN (VSV8)
I: PROTEIN (CD8A OR LYT2 OR LYT-2)
K: PROTEIN (CD8A OR LYT2 OR LYT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7767
Polymers73,3345
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.900, 98.400, 170.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)


Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01901
#2: Protein PROTEIN (BETA-2-MICROGLOBULIN )


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01887
#3: Protein/peptide PROTEIN (VSV8)


Mass: 956.078 Da / Num. of mol.: 2 / Fragment: ANTIGENIC PEPTIDE / Source method: obtained synthetically
#4: Protein
PROTEIN (CD8A OR LYT2 OR LYT-2)


Mass: 14512.637 Da / Num. of mol.: 4 / Fragment: IG ECTODOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: GENE FUSED TO THROMBIN CLEAVAGE SITE AND LEUCINE ZIPPER
Cell line (production host): CHO LEC 3.2.8.1 / Gene (production host): CD8A / Production host: Mus musculus (house mouse) / References: UniProt: P01731
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.5 / Details: 20-25% PEG 4K, 0.2M LI2SO4, 0.1M TRIS PH8.5
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMHEPES1drop
320-25 %PEG40001reservoir
40.2 M1reservoirLi2SO4
50.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 34131 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.061 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.249 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 99259 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 90.7 % / Rmerge(I) obs: 0.249

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VAA

2vaa


Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3285 10.1 %RANDOM
Rwork0.212 ---
obs0.212 32467 88.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10148 0 56 0 10204
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_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.511
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH3.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.511

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