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- PDB-3dmm: Crystal structure of the CD8 alpha beta/H-2Dd complex -

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Basic information

Entry
Database: PDB / ID: 3dmm
TitleCrystal structure of the CD8 alpha beta/H-2Dd complex
Components
  • (T-cell surface glycoprotein CD8 ...) x 2
  • Beta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Synthetic peptidePeptide synthesis
KeywordsIMMUNE SYSTEM / T cell co-receptor CD8ab MHC complex / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Secreted / Envelope protein / Alternative splicing / Polymorphism
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / 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 / regulation of membrane depolarization ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / 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 / regulation of membrane depolarization / MHC class I protein binding / plasma membrane raft / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / Neutrophil degranulation / 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 / calcium-mediated signaling / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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 immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / defense response to virus / intracellular iron ion homeostasis / adaptive immune response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / protein kinase binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
T-cell surface glycoprotein CD8 beta chain / 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 ...T-cell surface glycoprotein CD8 beta chain / 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, D-D alpha chain / T-cell surface glycoprotein CD8 beta chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, R. / Natarajan, K. / Margulies, D.H.
CitationJournal: J.Immunol. / Year: 2009
Title: Structural basis of the CD8alphabeta/MHC class i interaction: focused recognition orients CD8beta to a T cell proximal position.
Authors: Wang, R. / Natarajan, K. / Margulies, D.H.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2 microglobulin
P: Synthetic peptide
C: T-cell surface glycoprotein CD8 alpha chain
D: T-cell surface glycoprotein CD8 beta chain


Theoretical massNumber of molelcules
Total (without water)80,1205
Polymers80,1205
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-33.8 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.468, 96.694, 97.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT IS THE BIOLOGICAL COMPLEX, CONSISTING OF CHAINS A,B,P,C,D.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 32007.609 Da / Num. of mol.: 1 / Fragment: Alpha-1,2,3 regions: Residues 26-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P01900
#2: Protein Beta-2 microglobulin /


Mass: 11791.545 Da / Num. of mol.: 1 / Fragment: Residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS

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T-cell surface glycoprotein CD8 ... , 2 types, 2 molecules CD

#4: Protein T-cell surface glycoprotein CD8 alpha chain / T-cell surface glycoprotein Lyt-2 / CD8a antigen


Mass: 18361.881 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain: Residues 28-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8a, Lyt-2, Lyt2 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P01731
#5: Protein T-cell surface glycoprotein CD8 beta chain / T-cell surface glycoprotein Lyt-3 / T-cell membrane glycoprotein Ly-3 / Lymphocyte antigen 3 / CD8b antigen


Mass: 16883.535 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain: Residues 22-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8b, Cd8b1, Ly-3, Lyt-3, Lyt3 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P10300

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Protein/peptide / Non-polymers , 2 types, 38 molecules P

#3: Protein/peptide Synthetic peptide / Peptide synthesis


Mass: 1075.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 12% PEG 3000, 0.05M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 22842 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.45
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.6 / % possible all: 76.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1QO3, 2ATP

1qo3

2atp


Resolution: 2.6→43.32 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 92554.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1277 5.9 %RANDOM
Rwork0.248 ---
obs0.248 21800 91.8 %-
all-21800 --
Solvent computationSolvent model: FLAT / Bsol: 63.66 Å2 / ksol: 0.409086 e/Å3
Displacement parametersBiso mean: 54.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.731 Å20 Å20 Å2
2--3.487 Å20 Å2
3----17.218 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 0 37 5096
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.991.5
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scbond_it2.662
X-RAY DIFFRACTIONc_scangle_it4.22.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 155 5.7 %
Rwork0.364 2541 -
obs--69.6 %

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