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- PDB-7r7z: Crystal structure of QW9-HLA-B*5301 specific T Cell Receptor, C3 -

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Basic information

Entry
Database: PDB / ID: 7r7z
TitleCrystal structure of QW9-HLA-B*5301 specific T Cell Receptor, C3
Components
  • Alpha chain of C3 TCR
  • Beta chain of C3 TCR
KeywordsIMMUNE SYSTEM / MHC / T Cell Immunity / Antigen Presentation / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.286 Å
AuthorsLi, X.L. / Tan, K.M. / Xu, S.T. / Ng, R. / Walker, B.D. / Wang, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 HL103526; R01 AI149704; 5UM1Al144462; P30 AI060354 United States
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide.
Authors: Li, X. / Singh, N.K. / Collins, D.R. / Ng, R. / Zhang, A. / Lamothe-Molina, P.A. / Shahinian, P. / Xu, S. / Tan, K. / Piechocka-Trocha, A. / Urbach, J.M. / Weber, J.K. / Gaiha, G.D. / Takou ...Authors: Li, X. / Singh, N.K. / Collins, D.R. / Ng, R. / Zhang, A. / Lamothe-Molina, P.A. / Shahinian, P. / Xu, S. / Tan, K. / Piechocka-Trocha, A. / Urbach, J.M. / Weber, J.K. / Gaiha, G.D. / Takou Mbah, O.C. / Huynh, T. / Cheever, S. / Chen, J. / Birnbaum, M. / Zhou, R. / Walker, B.D. / Wang, J.H.
History
DepositionJun 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha chain of C3 TCR
B: Beta chain of C3 TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5926
Polymers50,0212
Non-polymers5714
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-63 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.156, 59.381, 82.675
Angle α, β, γ (deg.)90.000, 90.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha chain of C3 TCR


Mass: 22561.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Beta chain of C3 TCR


Mass: 27459.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 1.0 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate/citric acid, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 18393 / % possible obs: 98.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 32.18 Å2 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.07 / Rrim(I) all: 0.165 / Χ2: 0.907 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.382.60.86616830.490.5551.0350.81790.2
2.38-2.483.50.79817680.6480.4430.9160.79296.2
2.48-2.594.60.78718310.7350.3840.8780.82198.2
2.59-2.735.50.67118710.820.3040.7380.87699.2
2.73-2.95.80.46118520.9080.2040.5050.93999.3
2.9-3.125.90.27218310.9510.1210.2981.01899.4
3.12-3.445.80.17318690.9770.0780.191.05199.6
3.44-3.935.70.10518880.9850.0480.1160.98299.7
3.93-4.955.60.06618820.9930.0310.0740.86599.7
4.95-505.40.06119180.9930.0290.0680.75399.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OGA

1oga


Resolution: 2.286→41.336 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 914 5.29 %
Rwork0.2145 16361 -
obs0.2165 17275 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.44 Å2 / Biso mean: 40.6356 Å2 / Biso min: 12.85 Å2
Refinement stepCycle: final / Resolution: 2.286→41.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 22 83 3552
Biso mean--38.06 34.65 -
Num. residues----445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023549
X-RAY DIFFRACTIONf_angle_d0.534830
X-RAY DIFFRACTIONf_chiral_restr0.041529
X-RAY DIFFRACTIONf_plane_restr0.003632
X-RAY DIFFRACTIONf_dihedral_angle_d14.0922124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2861-2.40670.3033570.2784138453
2.4067-2.55740.30151390.2769214484
2.5574-2.75480.30811260.2713250297
2.7548-3.0320.29421760.2523251699
3.032-3.47050.2581570.22142567100
3.4705-4.37170.22761340.18592600100
4.3717-41.330.20191250.1796264899
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)
13.35530.67182.99322.1877-0.01957.9724-0.04530.00890.27840.10570.05590.1186-0.3434-0.1419-0.00990.16210.02880.06380.16540.01750.221385.48389.6991.8946
20.7021-0.3836-0.217.50170.50521.9526-0.04770.0826-0.00180.15970.099-0.3862-0.09040.084-0.05620.1047-0.009-0.04020.2113-0.00540.163698.2671-13.013109.0326
32.41290.2214-0.54116.9666-1.52183.8236-0.10620.1096-0.0442-0.2450.11890.46120.0341-0.37020.00610.1769-0.0278-0.01410.29260.00280.164969.5241-6.264690.9042
47.1556-0.3492-0.3717.46280.17856.21960.1396-0.59760.22990.40050.02310.1159-0.3584-0.3569-0.02930.30210.00930.05520.2256-0.02390.182785.8983-22.3678116.8303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 116 )B2 - 116
2X-RAY DIFFRACTION2chain 'B' and (resid 117 through 244 )B117 - 244
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 113 )A1 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 204)A114 - 204

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