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- PDB-2atp: Crystal structure of a CD8ab heterodimer -

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Basic information

Entry
Database: PDB / ID: 2atp
TitleCrystal structure of a CD8ab heterodimer
Components
  • T-cell surface glycoprotein CD8 alpha chain
  • T-cell surface glycoprotein CD8 beta chain
  • artifact linker
KeywordsIMMUNE SYSTEM / CD8ab / CD8aa / MHC
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane raft / MHC class I protein binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane raft / MHC class I protein binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling / T cell receptor signaling pathway / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / receptor complex / external side of plasma membrane / protein kinase binding / cell surface / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface glycoprotein CD8 beta chain / CD8 alpha subunit / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...T-cell surface glycoprotein CD8 beta chain / CD8 alpha subunit / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain / T-cell surface glycoprotein CD8 beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, H.C. / Tan, K. / Ouyang, J. / Parisini, E. / Liu, J.H. / Le, Y. / Wang, X. / Reinherz, E.L. / Wang, J.H.
CitationJournal: Immunity / Year: 2005
Title: Structural and Mutational Analyses of a CD8alphabeta Heterodimer and Comparison with the CD8alphaalpha Homodimer.
Authors: Chang, H.C. / Tan, K. / Ouyang, J. / Parisini, E. / Liu, J.H. / Le, Y. / Wang, X. / Reinherz, E.L. / Wang, J.H.
History
DepositionAug 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD8 alpha chain
E: artifact linker
B: T-cell surface glycoprotein CD8 beta chain
C: T-cell surface glycoprotein CD8 alpha chain
F: artifact linker
D: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4849
Polymers59,8206
Non-polymers6643
Water79344
1
A: T-cell surface glycoprotein CD8 alpha chain
E: artifact linker
B: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1314
Polymers29,9103
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-cell surface glycoprotein CD8 alpha chain
F: artifact linker
D: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3525
Polymers29,9103
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.668, 92.655, 79.330
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-cell surface glycoprotein CD8 alpha chain / T-cell surface glycoprotein Lyt-2


Mass: 13842.911 Da / Num. of mol.: 2 / Fragment: CD8a ectodomain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8a, Lyt-2, Lyt2 / Plasmid: pEE14 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-Lec 3.8.2.1 / References: UniProt: P01731
#2: Protein/peptide artifact linker


Mass: 3028.172 Da / Num. of mol.: 2
Fragment: a peptide used to connect CD8a C-terminal and CD8b N-terminal
Source method: obtained synthetically / Details: synthetic linker
#3: Protein T-cell surface glycoprotein CD8 beta chain / T-cell surface glycoprotein Lyt-3 / T-cell membrane glycoprotein Ly-3


Mass: 13038.967 Da / Num. of mol.: 2 / Fragment: CD8b ectodomain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8b, Lyt-3, Lyt3 / Plasmid: pEE14 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-Lec 3.8.2.1 / References: UniProt: P10300
#4: 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.: 3
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG4000, 0.2M (NH4)2SO4, 0.1 M Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 21001 / Num. obs: 21001 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2071 / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BQH

1bqh


Resolution: 2.4→25 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1497 -RANDOM
Rwork0.242 ---
obs0.246 19292 90.9 %-
all-20984 --
Displacement parametersBiso mean: 52.314 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 42 44 3836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0092
X-RAY DIFFRACTIONc_angle_deg1.913
X-RAY DIFFRACTIONc_dihedral_angle_d27.842
X-RAY DIFFRACTIONc_improper_angle_d1.649
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection
Rfree0.457 121
Rwork0.406 -
obs-1550

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