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- PDB-3b9k: Crystal structure of CD8alpha-beta in complex with YTS 156.7 FAB -

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Basic information

Entry
Database: PDB / ID: 3b9k
TitleCrystal structure of CD8alpha-beta in complex with YTS 156.7 FAB
Components
  • (T-cell surface glycoprotein CD8 ...) x 2
  • Fab Heavy chainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / V-set / IgSF dimer / Glycoprotein / Immune response / Membrane / Transmembrane
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)
rattus rattus (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsShore, D. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Crystal Structure of CD8 in Complex with YTS156.7.7 Fab and Interaction with Other CD8 Antibodies Define the Binding Mode of CD8 alphabeta to MHC Class I
Authors: Shore, D.A. / Issafras, H. / Landais, E. / Teyton, L. / Wilson, I.A.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Jun 22, 2016Group: Structure summary
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab Light Chain
H: Fab Heavy chain
A: T-cell surface glycoprotein CD8 alpha chain
B: T-cell surface glycoprotein CD8 beta chain
C: Fab Light Chain
D: Fab Heavy chain
E: T-cell surface glycoprotein CD8 alpha chain
F: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,81710
Polymers150,3758
Non-polymers4422
Water64936
1
L: Fab Light Chain
H: Fab Heavy chain
A: T-cell surface glycoprotein CD8 alpha chain
B: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4095
Polymers75,1874
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-40 kcal/mol
Surface area30590 Å2
MethodPISA
2
C: Fab Light Chain
D: Fab Heavy chain
E: T-cell surface glycoprotein CD8 alpha chain
F: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4095
Polymers75,1874
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-44 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.779, 92.747, 190.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21D
12L
22D
13H
23B
14H
24B
15C
25A
16F
26E

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRALALA5 - 1005 - 99
221GLNTYRDF5 - 1005 - 103
112ASPTHRLA110 - 200109 - 199
222THRPRODF110 - 200114 - 191
113GLNTHRHB5 - 1105 - 114
223PROVALBD5 - 1175 - 117
114SERVALHB120 - 210124 - 199
115THRGLUCE5 - 1055 - 104
225PROILEAC5 - 1055 - 105
216ALALYSEG4 - 1214 - 121

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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T-cell surface glycoprotein CD8 ... , 2 types, 4 molecules AEBF

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


Mass: 14783.935 Da / Num. of mol.: 2 / Fragment: Ig-like V-type domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8a, Lyt-2, Lyt2 / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 / References: UniProt: P01731
#4: 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: 14080.103 Da / Num. of mol.: 2 / Fragment: Ig-like V-type domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8b, Cd8b1, Ly-3, Lyt-3, Lyt3 / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 / References: UniProt: P10300

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Antibody , 2 types, 4 molecules LCHD

#1: Antibody Fab Light Chain / Fragment antigen-binding


Mass: 23459.062 Da / Num. of mol.: 2 / Fragment: Fab Fragment / Source method: isolated from a natural source / Source: (natural) rattus rattus (black rat) / Cell line: hybridoma / Strain: YTS156.7
#2: Antibody Fab Heavy chain / Fragment antigen-binding


Mass: 22864.342 Da / Num. of mol.: 2 / Fragment: Fab Fragment / Source method: isolated from a natural source / Source: (natural) rattus rattus (black rat) / Cell line: hybridoma / Strain: YTS156.7

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Sugars / Non-polymers , 2 types, 38 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 296 K / Method: sitting drop / pH: 6.2
Details: PEG 8000, 0.1 M Na/K phosphate, 0.2 M NaCl, pH 6.2, sitting drop, temperature 296K

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Data collection

DiffractionMean temperature: 93.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2005
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 9.6 / Number: 147032 / Rmerge(I) obs: 0.131 / Χ2: 1.04 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 44334 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.815091.710.0620.967
4.625.8194.110.1021.072
4.034.6294.910.1211.078
3.664.0396.710.161.028
3.43.669910.1961
3.23.499.810.2010.978
3.043.299.910.2511.061
2.913.0499.810.3241.056
2.82.9199.910.4271.083
2.72.899.810.5791.078
ReflectionResolution: 2.7→50 Å / Num. obs: 45395 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.04 / Net I/σ(I): 9.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.17 / Num. unique all: 4468 / Χ2: 1.078 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.33 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 32.285 / SU ML: 0.327 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.22 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2216 5 %RANDOM
Rwork0.235 ---
obs0.238 42077 97.57 %-
all-42077 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.349 Å2
Baniso -1Baniso -2Baniso -3
1--3.44 Å20 Å20 Å2
2--2.26 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10234 0 28 36 10298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210500
X-RAY DIFFRACTIONr_bond_other_d0.0070.027042
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.95714262
X-RAY DIFFRACTIONr_angle_other_deg0.9073.00217238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61251316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95824.417412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.508151768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6091540
X-RAY DIFFRACTIONr_chiral_restr0.0860.21626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022058
X-RAY DIFFRACTIONr_nbd_refined0.2380.21903
X-RAY DIFFRACTIONr_nbd_other0.2150.26879
X-RAY DIFFRACTIONr_nbtor_refined0.1880.24915
X-RAY DIFFRACTIONr_nbtor_other0.0910.25890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0830.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.28
X-RAY DIFFRACTIONr_mcbond_it2.45238295
X-RAY DIFFRACTIONr_mcbond_other0.32432656
X-RAY DIFFRACTIONr_mcangle_it2.847510730
X-RAY DIFFRACTIONr_scbond_it5.14584653
X-RAY DIFFRACTIONr_scangle_it6.595113532
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L1232LOOSE POSITIONAL0.345
2L1182LOOSE POSITIONAL0.415
3H1400LOOSE POSITIONAL0.375
4H1069LOOSE POSITIONAL0.45
5C1381LOOSE POSITIONAL0.495
6F1340LOOSE POSITIONAL0.45
1L1232LOOSE THERMAL2.1910
2L1182LOOSE THERMAL3.0910
3H1400LOOSE THERMAL2.3310
4H1069LOOSE THERMAL3.4810
5C1381LOOSE THERMAL210
6F1340LOOSE THERMAL2.210
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 176 -
Rwork0.35 3110 -
all-3286 -
obs--99.76 %
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)
12.047-0.158-0.11482.3459-1.39183.7626-0.06410.1236-0.2313-0.09540.11190.19920.185-0.0949-0.04780.0436-0.05370.0256-0.2441-0.0368-0.1367-11.457-52.99328.988
23.7105-1.3326-1.14872.85980.14864.23740.01890.07480.23890.0694-0.0448-0.0833-0.3646-0.02580.02590.1454-0.0606-0.0434-0.1790.0246-0.1106-10.893-31.57722.646
35.26631.0535-1.50557.3194-0.17063.55860.1363-0.5768-0.17061.8856-0.22490.9634-0.13940.1280.08860.4023-0.09330.327-0.64880.0556-0.142-24.77-31.20357.438
43.6763-3.4059-1.47779.73191.60694.35080.00910.0265-0.06520.54490.28882.29570.0067-0.3773-0.29790.0298-0.1130.3965-0.72580.06540.524-35.822-41.37453.551
52.90650.2779-0.41722.9795-1.824.5673-0.03780.0716-0.105-0.0562-0.01220.08960.26210.01490.050.04-0.0270.0343-0.3486-0.0589-0.188-11.574-99.06743.431
67.7354-3.4514-2.504910.01692.96111.4374-0.4197-0.1947-0.14641.61060.68612.2848-0.4335-0.6874-0.26640.44130.29390.5748-0.21320.34220.3543-36.817-89.71667.272
70.8145-0.0568-1.56494.08130.17084.49510.16350.01440.16120.21560.03810.0749-0.3888-0.0256-0.20160.0866-0.01020.0429-0.23270.0277-0.074-11.183-77.48537.897
88.1254-2.33290.219612.4945-8.883117.5056-0.6291-1.11410.36083.30120.9273-0.3995-1.62520.1229-0.29831.13690.43720.1779-0.3599-0.1631-0.0221-26.653-78.67872.163
98.9485-1.7767-1.82373.65031.09325.63590.1660.9206-0.6294-0.0664-0.17560.28950.19870.03770.0096-0.24760.02210.0262-0.053-0.0634-0.279715.777-95.2175.47
106.9845-0.4207-1.20564.34431.03654.85890.04370.6617-0.70420.0213-0.25630.25720.3271-0.02370.2127-0.2584-0.0060.03270.0135-0.0908-0.29615.768-50.32-9.373
113.4630.65040.61242.19550.42262.4565-0.13720.52880.2586-0.14330.0543-0.0315-0.18970.16350.0829-0.0816-0.01130.08320.01790.0225-0.183-2.792-84.85511.902
123.67860.160.5552.0390.4554.2916-0.00830.67050.2767-0.2049-0.0372-0.0261-0.24290.32040.0455-0.0845-0.01410.05580.00480.0381-0.2449-2.677-39.873-3.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION2H1 - 110
3X-RAY DIFFRACTION3H121 - 210
4X-RAY DIFFRACTION4L110 - 210
5X-RAY DIFFRACTION5D1 - 109
6X-RAY DIFFRACTION6D110 - 210
7X-RAY DIFFRACTION7B1 - 110
8X-RAY DIFFRACTION8B121 - 210
9X-RAY DIFFRACTION9A4 - 110
10X-RAY DIFFRACTION10C4 - 110
11X-RAY DIFFRACTION11E4 - 110
12X-RAY DIFFRACTION12R1 - 110

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