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- PDB-8rvd: Unbound murine diabetogenic 4.1 TCR -

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Basic information

Entry
Database: PDB / ID: 8rvd
TitleUnbound murine diabetogenic 4.1 TCR
Components
  • 4.1 TCR alpha chain
  • 4.1 TCR beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / autoreactive / type I diabetes
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLopez-Sagaseta, J. / Erausquin, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
CitationJournal: To Be Published
Title: Unbound murine diabetogenic 4.1 TCR
Authors: Lopez-Sagaseta, J. / Erausquin, E.
History
DepositionFeb 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 4.1 TCR beta chain
H: 4.1 TCR alpha chain
A: 4.1 TCR beta chain
B: 4.1 TCR alpha chain
C: 4.1 TCR beta chain
D: 4.1 TCR alpha chain
F: 4.1 TCR beta chain
G: 4.1 TCR alpha chain
I: 4.1 TCR beta chain
J: 4.1 TCR alpha chain
K: 4.1 TCR beta chain
L: 4.1 TCR alpha chain
M: 4.1 TCR beta chain
N: 4.1 TCR alpha chain
O: 4.1 TCR beta chain
P: 4.1 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,84025
Polymers404,01816
Non-polymers8229
Water00
1
E: 4.1 TCR beta chain
H: 4.1 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5973
Polymers50,5022
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-32 kcal/mol
Surface area20450 Å2
MethodPISA
2
A: 4.1 TCR beta chain
B: 4.1 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6924
Polymers50,5022
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-37 kcal/mol
Surface area20480 Å2
MethodPISA
3
C: 4.1 TCR beta chain
D: 4.1 TCR alpha chain


Theoretical massNumber of molelcules
Total (without water)50,5022
Polymers50,5022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-28 kcal/mol
Surface area19730 Å2
MethodPISA
4
F: 4.1 TCR beta chain
G: 4.1 TCR alpha chain


Theoretical massNumber of molelcules
Total (without water)50,5022
Polymers50,5022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-25 kcal/mol
Surface area20920 Å2
MethodPISA
5
I: 4.1 TCR beta chain
J: 4.1 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6924
Polymers50,5022
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-32 kcal/mol
Surface area20650 Å2
MethodPISA
6
K: 4.1 TCR beta chain
L: 4.1 TCR alpha chain


Theoretical massNumber of molelcules
Total (without water)50,5022
Polymers50,5022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-25 kcal/mol
Surface area20110 Å2
MethodPISA
7
M: 4.1 TCR beta chain
N: 4.1 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5973
Polymers50,5022
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-23 kcal/mol
Surface area20140 Å2
MethodPISA
8
O: 4.1 TCR beta chain
P: 4.1 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7545
Polymers50,5022
Non-polymers2523
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-32 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.986, 151.131, 135.550
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4.1 TCR beta chain


Mass: 27323.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein
4.1 TCR alpha chain


Mass: 23178.820 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium phosphate (NaH2PO4) pH 6.5, 14% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 25, 2023
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→151.13 Å / Num. obs: 90351 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.114 / Rrim(I) all: 0.213 / Χ2: 0.96 / Net I/σ(I): 6.2
Reflection shellResolution: 3.15→3.2 Å / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.385 / Num. measured all: 15523 / Num. unique obs: 4447 / CC1/2: 0.446 / Rpim(I) all: 0.87 / Rrim(I) all: 1.639 / Χ2: 0.93 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→135.39 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 14.553 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26619 4340 4.8 %RANDOM
Rwork0.21649 ---
obs0.21889 85986 86.27 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.606 Å2
Baniso -1Baniso -2Baniso -3
1-42.72 Å20 Å2-5.47 Å2
2--0.51 Å2-0 Å2
3----43.23 Å2
Refinement stepCycle: 1 / Resolution: 3→135.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25675 0 44 0 25719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01226369
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.79536028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27853415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.7875139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.201103600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.24017
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220793
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.3386.88113756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.99412.31717139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.7626.9612613
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.0783.69102379
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %

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