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Basic information

Entry
Database: PDB / ID: 2hp4
TitleComputational design and crystal structure of an enhanced affinity mutant human CD8-alpha-alpha co-receptor
ComponentsT-cell surface glycoprotein CD8 alpha chain
KeywordsIMMUNE SYSTEM / CD8 / Co-receptor / Soluble protein / KD / Protein engineering / Immunotherapy / Immune-suppressor
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / T cell receptor complex / MHC class I protein binding / plasma membrane raft / antigen processing and presentation / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / T cell receptor complex / MHC class I protein binding / plasma membrane raft / antigen processing and presentation / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor signaling pathway / adaptive immune response / cell surface receptor signaling pathway / receptor complex / immune response / external side of plasma membrane / extracellular region / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Jakobsen, B.K. / Boulter, J.M. / Glick, M. / Gao, G.F.
CitationJournal: Proteins / Year: 2007
Title: Computational design and crystal structure of an enhanced affinity mutant human CD8 alphaalpha coreceptor
Authors: Cole, D.K. / Rizkallah, P.J. / Boulter, J.M. / Sami, M. / Vuidepot, A.-L. / Glick, M. / Gao, F. / Bell, J.I. / Jakobsen, B.K. / Gao, G.F.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,53811
Polymers25,6892
Non-polymers8499
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-75 kcal/mol
Surface area11670 Å2
MethodPISA
2
A: T-cell surface glycoprotein CD8 alpha chain
hetero molecules

A: T-cell surface glycoprotein CD8 alpha chain
hetero molecules

B: T-cell surface glycoprotein CD8 alpha chain
hetero molecules

B: T-cell surface glycoprotein CD8 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,07522
Polymers51,3784
Non-polymers1,69718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
crystal symmetry operation5_555y,-x+y,z+1/31
Buried area7260 Å2
ΔGint-151 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.723, 99.723, 55.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-439-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31B
41A

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROBB1 - 391 - 39
21PROPROAA1 - 391 - 39
32ALAALABB45 - 11445 - 114
42ALAALAAA45 - 11445 - 114

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Components

#1: Protein T-cell surface glycoprotein CD8 alpha chain / T-lymphocyte differentiation antigen T8/Leu-2 / CD8a antigen


Mass: 12844.512 Da / Num. of mol.: 2 / Fragment: HLA Co-receptor, Ig-like V-type / Mutation: C33A/S53N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBJ112 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01732
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 25.5% PEG 8000, 0.085M Sodium Cacodylate, 0.17M Ammonium Sulphate, 15% Glycerol, 3% Ethylene Glycol, pH 6.50, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2003
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→29.185 Å / Num. obs: 19090 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.17 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 8.95
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.04 / % possible all: 94.84

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Phasing

Phasing MRRfactor: 0.376 / Cor.coef. Fo:Fc: 0.656
Highest resolutionLowest resolution
Rotation3 Å28.79 Å
Translation3 Å28.79 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.5data scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CD8

1cd8


Resolution: 2.1→29.185 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.06 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23316 930 5.1 %RANDOM
Rwork0.18217 ---
obs0.18464 17444 98.54 %-
all-18374 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 49 282 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221926
X-RAY DIFFRACTIONr_bond_other_d0.0030.021326
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9782620
X-RAY DIFFRACTIONr_angle_other_deg0.72233204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0775234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.1522.95588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.33115296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4711514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_nbd_refined0.2050.3321
X-RAY DIFFRACTIONr_nbd_other0.2160.31406
X-RAY DIFFRACTIONr_nbtor_refined0.1890.5898
X-RAY DIFFRACTIONr_nbtor_other0.0920.5995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.5304
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2080.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.550
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.46121444
X-RAY DIFFRACTIONr_mcbond_other0.5842458
X-RAY DIFFRACTIONr_mcangle_it2.96231858
X-RAY DIFFRACTIONr_scbond_it4.0784920
X-RAY DIFFRACTIONr_scangle_it5.3336758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1513 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.20.5
medium thermal0.692
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 66 -
Rwork0.229 1246 -
obs--94.19 %
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)
12.03740.1496-0.22870.8444-0.06220.96710.00640.0557-0.0417-0.04150.0141-0.02580.0240.0291-0.0205-0.1780.0123-0.0165-0.1388-0.002-0.186711.548639.7464-0.1095
22.054-0.1801-0.01410.89720.14071.1540.009-0.1009-0.05050.03380.0118-0.00110.039-0.0581-0.0208-0.1813-0.0127-0.0113-0.1480.0022-0.1911-11.576739.74993.3476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 391 - 39
2X-RAY DIFFRACTION1AA45 - 11445 - 114
3X-RAY DIFFRACTION2BB1 - 391 - 39
4X-RAY DIFFRACTION2BB45 - 11445 - 114

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