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- PDB-5ebg: Crystal structure of bovine CD8aa homodimer -

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Basic information

Entry
Database: PDB / ID: 5ebg
TitleCrystal structure of bovine CD8aa homodimer
ComponentsT-cell surface glycoprotein CD8 alpha chain
KeywordsIMMUNE SYSTEM / bovine / CD8alpha / homodimer / immunology
Function / homology
Function and homology information


cytotoxic T cell differentiation / T cell mediated immunity / membrane => GO:0016020 / cell surface receptor signaling pathway / external side of plasma membrane
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y. / Li, X. / Zhang, N. / Qi, J. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
973ProjectNO. 2013CB835302 China
CitationJournal: Sci Rep / Year: 2016
Title: The structural basis of chicken, swine and bovine CD8 alpha alpha dimers provides insight into the co-evolution with MHC I in endotherm species.
Authors: Liu, Y. / Li, X. / Qi, J. / Zhang, N. / Xia, C.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Item: _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: T-cell surface glycoprotein CD8 alpha chain
B: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)25,8802
Polymers25,8802
Non-polymers00
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint0 kcal/mol
Surface area12870 Å2
Unit cell
Length a, b, c (Å)74.415, 74.415, 143.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-297-

HOH

21A-356-

HOH

31A-396-

HOH

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Components

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


Mass: 12939.822 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P31783
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris pH6.5, 20% v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21811 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 41
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 5.364 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.5_2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CD8

1cd8


Resolution: 1.8→32.223 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 0.26 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 1110 5.09 %
Rwork0.1979 --
obs0.1988 21811 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.258 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1122 Å20 Å20 Å2
2---1.1122 Å2-0 Å2
3---2.2244 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 0 365 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011859
X-RAY DIFFRACTIONf_angle_d1.1592514
X-RAY DIFFRACTIONf_dihedral_angle_d17.769683
X-RAY DIFFRACTIONf_chiral_restr0.08275
X-RAY DIFFRACTIONf_plane_restr0.004325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.88170.28151220.20352405X-RAY DIFFRACTION92
1.8817-1.98090.20161290.19912458X-RAY DIFFRACTION94
1.9809-2.1050.24211370.19252525X-RAY DIFFRACTION97
2.105-2.26750.2581430.20432560X-RAY DIFFRACTION97
2.2675-2.49560.22891460.22052556X-RAY DIFFRACTION97
2.4956-2.85650.23481490.21952621X-RAY DIFFRACTION98
2.8565-3.59810.19271550.18132681X-RAY DIFFRACTION99
3.5981-32.22780.17721290.17962895X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0446-0.043-0.00390.06040.05040.1097-0.018-0.0274-0.02590.01360.0162-0.00860.08040.02230.02890.0566-0.00310.00350.06580.01140.058-21.514512.66576.1613
20.0265-0.0383-0.01310.05440.01190.0546-0.0515-0.0686-0.0201-0.08930.00530.0259-0.0642-0.0287-0.03530.0607-0.00740.00820.0680.00630.0722-27.262525.31395.514
30.1005-0.0514-0.00120.1750.08420.1030.02750.29880.106-0.25590.06860.15830.0914-0.24420.00610.18380.0033-0.00870.15950.02240.1313-33.84319.4769-4.8562
40.1324-0.0488-0.02860.42780.010.1786-0.02460.00970.02740.03640.01240.10910.05680.0067-0.1230.0665-0.00740.00350.06290.00950.0684-24.361318.36084.9514
50.1530.0472-0.01370.1038-0.00770.1104-0.0384-0.01620.040.02420.02460.02990.05060.0497-0.02010.08450.0083-0.0090.08430.01860.0763-15.965413.492928.3346
60.22460.0606-0.02090.02360.02280.0983-0.1216-0.0690.03110.12440.0609-0.04940.10450.0146-0.03440.10850.01420.02240.1276-0.01270.0925-4.575217.718632.7233
70.0631-0.0659-0.02840.18020.01250.07860.00640.04460.1211-0.10510.03880.0099-0.00590.01530.03890.0698-0.0079-0.00740.10010.00790.0813-8.40523.850923.3015
80.506-0.21950.09160.16220.05740.1152-0.0521-0.04050.06390.00470.1133-0.04230.02730.16750.01230.07890.0077-0.01310.10850.00740.0714-7.30913.730729.8663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:33)
2X-RAY DIFFRACTION2chain 'A' and (resseq 34:53)
3X-RAY DIFFRACTION3chain 'A' and (resseq 54:68)
4X-RAY DIFFRACTION4chain 'A' and (resseq 69:115)
5X-RAY DIFFRACTION5chain 'B' and (resseq 2:25)
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:47)
7X-RAY DIFFRACTION7chain 'B' and (resseq 48:83)
8X-RAY DIFFRACTION8chain 'B' and (resseq 84:115)

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