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- PDB-8ro5: HLA-A3 restricted mG12V-TCR -

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Basic information

Entry
Database: PDB / ID: 8ro5
TitleHLA-A3 restricted mG12V-TCR
Components
  • Chains: A
  • Chains: B
KeywordsIMMUNE SYSTEM / HLA-A*03:01 with KRAS-G12V-10mer
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSim, M.J.W. / Sun, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Eur.J.Immunol. / Year: 2024
Title: Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3.
Authors: Sim, M.J.W. / Hanada, K.I. / Stotz, Z. / Yu, Z. / Lu, J. / Brennan, P. / Quastel, M. / Gillespie, G.M. / Long, E.O. / Yang, J.C. / Sun, P.D.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chains: B
A: Chains: A


Theoretical massNumber of molelcules
Total (without water)50,4532
Polymers50,4532
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-28 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.575, 43.320, 84.243
Angle α, β, γ (deg.)90.000, 108.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Chains: B


Mass: 27680.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Chains: A


Mass: 22773.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: n

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→40.2 Å / Num. obs: 51656 / % possible obs: 99.06 % / Redundancy: 1.05 % / Biso Wilson estimate: 17.63 Å2 / CC1/2: 1 / Net I/σ(I): 16.88
Reflection shellResolution: 1.701→1.762 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5022 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.2 Å / SU ML: 0.1929 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.9392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2093 2657 5.16 %
Rwork0.183 48845 -
obs0.1843 51502 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 0 351 3904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653644
X-RAY DIFFRACTIONf_angle_d0.99514957
X-RAY DIFFRACTIONf_chiral_restr0.0623539
X-RAY DIFFRACTIONf_plane_restr0.011643
X-RAY DIFFRACTIONf_dihedral_angle_d6.4943485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.33041620.27092476X-RAY DIFFRACTION96.99
1.73-1.770.27851070.24042514X-RAY DIFFRACTION97.73
1.77-1.80.27491380.21652560X-RAY DIFFRACTION98.07
1.8-1.840.22831370.20082507X-RAY DIFFRACTION98.36
1.84-1.880.2291420.1822567X-RAY DIFFRACTION98.62
1.88-1.930.23141330.17712505X-RAY DIFFRACTION98.65
1.93-1.980.19561260.17672595X-RAY DIFFRACTION99.02
1.98-2.040.21971390.18062528X-RAY DIFFRACTION99.03
2.04-2.110.22781350.18282564X-RAY DIFFRACTION99.08
2.11-2.180.23321500.19082542X-RAY DIFFRACTION99.08
2.18-2.270.20391270.18872605X-RAY DIFFRACTION99.35
2.27-2.370.21981640.19032552X-RAY DIFFRACTION99.45
2.37-2.50.24271440.19612552X-RAY DIFFRACTION99.56
2.5-2.650.22431410.19452579X-RAY DIFFRACTION99.63
2.65-2.860.22231650.19682608X-RAY DIFFRACTION99.96
2.86-3.150.17821270.18952612X-RAY DIFFRACTION99.93
3.15-3.60.16481380.172628X-RAY DIFFRACTION99.93
3.6-4.540.17491490.15362614X-RAY DIFFRACTION100
4.54-40.20.21321330.17452737X-RAY DIFFRACTION99.86

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