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- PDB-8yj3: N17.1.2 recognition of NRAS neoantigens -

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Basic information

Entry
Database: PDB / ID: 8yj3
TitleN17.1.2 recognition of NRAS neoantigens
Components
  • tcr alpha
  • tcr beta
KeywordsIMMUNE SYSTEM / T cell receptor / p-MHC
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsWu, D.C. / Mariuzza, R.A.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270995 China
National Natural Science Foundation of China (NSFC)32100985 China
CitationJournal: Sci Adv / Year: 2024
Title: Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens.
Authors: Wu, D. / Yin, R. / Chen, G. / Ribeiro-Filho, H.V. / Cheung, M. / Robbins, P.F. / Mariuzza, R.A. / Pierce, B.G.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: tcr beta
D: tcr alpha
A: tcr beta
B: tcr alpha
C: tcr beta
F: tcr alpha
G: tcr beta
H: tcr alpha


Theoretical massNumber of molelcules
Total (without water)205,0468
Polymers205,0468
Non-polymers00
Water00
1
E: tcr beta
D: tcr alpha


Theoretical massNumber of molelcules
Total (without water)51,2612
Polymers51,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-24 kcal/mol
Surface area21320 Å2
MethodPISA
2
A: tcr beta
B: tcr alpha


Theoretical massNumber of molelcules
Total (without water)51,2612
Polymers51,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-24 kcal/mol
Surface area21120 Å2
MethodPISA
3
C: tcr beta
F: tcr alpha


Theoretical massNumber of molelcules
Total (without water)51,2612
Polymers51,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-25 kcal/mol
Surface area21120 Å2
MethodPISA
4
G: tcr beta
H: tcr alpha


Theoretical massNumber of molelcules
Total (without water)51,2612
Polymers51,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-24 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.228, 66.113, 138.590
Angle α, β, γ (deg.)90.00, 97.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tcr beta


Mass: 28186.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: tcr beta / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
tcr alpha


Mass: 23074.811 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8mg/ml, 0.2 M MgCl2, 0.2M NaNO3, 14-18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→47.621 Å / Num. obs: 148044 / % possible obs: 97.7 % / Redundancy: 6.4 % / CC1/2: 0.953 / Rmerge(I) obs: 0.206 / Net I/σ(I): 9.8
Reflection shellResolution: 3.5→3.63 Å / Num. unique obs: 23156 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.503→47.621 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3156 1151 4.98 %
Rwork0.2579 --
obs0.2608 23098 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→47.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14248 0 0 0 14248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314604
X-RAY DIFFRACTIONf_angle_d0.65719860
X-RAY DIFFRACTIONf_dihedral_angle_d7.1548796
X-RAY DIFFRACTIONf_chiral_restr0.0472164
X-RAY DIFFRACTIONf_plane_restr0.0052580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.503-3.66220.37471550.32882692X-RAY DIFFRACTION97
3.6622-3.85520.37071490.33242710X-RAY DIFFRACTION98
3.8552-4.09660.38711230.31382779X-RAY DIFFRACTION98
4.0966-4.41270.34641380.28852618X-RAY DIFFRACTION94
4.4127-4.85640.33111450.25962735X-RAY DIFFRACTION98
4.8564-5.55820.29551570.24142800X-RAY DIFFRACTION99
5.5582-6.99920.32151410.25862802X-RAY DIFFRACTION99
6.9992-47.6210.2611430.20622811X-RAY DIFFRACTION96

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