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- PDB-4e42: Structural basis for the recognition of mutant self by a tumor-sp... -

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Basic information

Entry
Database: PDB / ID: 4.0E+42
TitleStructural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4
Components(T cell receptor G4 ...) x 2
KeywordsIMMUNE SYSTEM / Ig domain / adaptive immunity / T cell receptor / MHC
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NITRATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDeng, L. / Langley, R.J. / Wang, Q. / Topalian, S.L. / Mariuzza, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4
Authors: Deng, L. / Langley, R.J. / Wang, Q. / Topalian, S.L. / Mariuzza, R.A.
History
DepositionMar 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T cell receptor G4 alpha chain
B: T cell receptor G4 beta chain
C: T cell receptor G4 alpha chain
D: T cell receptor G4 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,13917
Polymers99,6504
Non-polymers48913
Water3,693205
1
A: T cell receptor G4 alpha chain
B: T cell receptor G4 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0879
Polymers49,8252
Non-polymers2627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-86 kcal/mol
Surface area19880 Å2
MethodPISA
2
C: T cell receptor G4 alpha chain
D: T cell receptor G4 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0528
Polymers49,8252
Non-polymers2276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-72 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.070, 75.365, 130.859
Angle α, β, γ (deg.)90.00, 123.48, 90.00
Int Tables number5
Space group name H-MC121
Detailsheterodimer

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Components

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T cell receptor G4 ... , 2 types, 4 molecules ACBD

#1: Protein T cell receptor G4 alpha chain


Mass: 22670.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein T cell receptor G4 beta chain


Mass: 27154.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 218 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 1.5 M sodium nitrate 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 37490 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 25.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 17.8 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E41

4e41


Resolution: 2.7→44.63 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.875 / SU B: 11.126 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.497 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26263 1908 5.1 %RANDOM
Rwork0.20033 ---
obs0.20347 35795 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.376 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-1.35 Å2
2--0.55 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 19 205 6845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9329268
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8785816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0124.31348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.274151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2651542
X-RAY DIFFRACTIONr_chiral_restr0.0870.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025319
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22783
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24489
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2360.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6431.54142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23526690
X-RAY DIFFRACTIONr_scbond_it1.46832805
X-RAY DIFFRACTIONr_scangle_it2.5464.52578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 138 -
Rwork0.3 2598 -
obs--99.85 %

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