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- PDB-6dfq: mouse diabetogenic TCR I.29 -

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Basic information

Entry
Database: PDB / ID: 6dfq
Titlemouse diabetogenic TCR I.29
Components
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / Type 1 Diabetes / Autoimmunity
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsWang, Y. / Dai, S.
CitationJournal: Sci Immunol / Year: 2019
Title: How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes.
Authors: Wang, Y. / Sosinowski, T. / Novikov, A. / Crawford, F. / White, J. / Jin, N. / Liu, Z. / Zou, J. / Neau, D. / Davidson, H.W. / Nakayama, M. / Kwok, W.W. / Gapin, L. / Marrack, P. / Kappler, J.W. / Dai, S.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TCR alpha chain
F: TCR beta chain
A: TCR alpha chain
B: TCR beta chain
C: TCR alpha chain
D: TCR beta chain
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,83311
Polymers204,6698
Non-polymers1643
Water3,027168
1
E: TCR alpha chain
F: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)51,1672
Polymers51,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-24 kcal/mol
Surface area20770 Å2
MethodPISA
2
A: TCR alpha chain
B: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)51,1672
Polymers51,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-32 kcal/mol
Surface area20570 Å2
MethodPISA
3
C: TCR alpha chain
D: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2073
Polymers51,1672
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-34 kcal/mol
Surface area20940 Å2
MethodPISA
4
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2914
Polymers51,1672
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-20 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.107, 117.629, 234.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21A
12E
22C
13E
23G
14F
24B
15F
25D
16F
26H
17A
27C
18A
28G
19B
29D
110B
210H
111C
211G
112D
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROEA2 - 2052 - 205
21GLUGLUPROPROAC2 - 2052 - 205
12GLUGLUPROPROEA2 - 2052 - 205
22GLUGLUPROPROCE2 - 2052 - 205
13GLUGLUALAALAEA2 - 1802 - 180
23GLUGLUALAALAGG2 - 1802 - 180
14LEULEUARGARGFB3 - 2403 - 240
24LEULEUARGARGBD3 - 2403 - 240
15LEULEUALAALAFB3 - 2413 - 241
25LEULEUALAALADF3 - 2413 - 241
16LEULEUALAALAFB3 - 2413 - 241
26LEULEUALAALAHH3 - 2413 - 241
17GLUGLUPROPROAC2 - 2052 - 205
27GLUGLUPROPROCE2 - 2052 - 205
18GLUGLUALAALAAC2 - 1802 - 180
28GLUGLUALAALAGG2 - 1802 - 180
19LEULEUARGARGBD3 - 2403 - 240
29LEULEUARGARGDF3 - 2403 - 240
110LEULEUALAALABD3 - 2413 - 241
210LEULEUALAALAHH3 - 2413 - 241
111GLUGLUALAALACE2 - 1802 - 180
211GLUGLUALAALAGG2 - 1802 - 180
112LEULEUALAALADF3 - 2413 - 241
212LEULEUALAALAHH3 - 2413 - 241

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
TCR alpha chain


Mass: 23361.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
#2: Protein
TCR beta chain


Mass: 27805.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% MPD, 100mM sodium cacodylate at pH6.0, 50mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 76175 / % possible obs: 98.13 % / Redundancy: 3.7 % / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→47.6 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.808 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25253 4079 5.1 %RANDOM
Rwork0.21985 ---
obs0.22153 76175 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.6→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13467 0 9 168 13644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01413846
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711911
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.74618851
X-RAY DIFFRACTIONr_angle_other_deg0.5311.70227931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.99451698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29920.237548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.078151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.941582
X-RAY DIFFRACTIONr_chiral_restr0.0690.21811
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022642
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_it6.1937.1916829
X-RAY DIFFRACTIONr_mcbond_other6.1927.1926830
X-RAY DIFFRACTIONr_mcangle_it9.52110.7748506
X-RAY DIFFRACTIONr_mcangle_other9.52110.7758507
X-RAY DIFFRACTIONr_scbond_it6.7487.6847017
X-RAY DIFFRACTIONr_scbond_other6.7477.6847017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.34211.31110343
X-RAY DIFFRACTIONr_long_range_B_refined14.50383.7514135
X-RAY DIFFRACTIONr_long_range_B_other14.50383.75214136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E53310.12
12A53310.12
21E54970.12
22C54970.12
31E45630.14
32G45630.14
41F72300.09
42B72300.09
51F71340.11
52D71340.11
61F69430.1
62H69430.1
71A53520.13
72C53520.13
81A45340.14
82G45340.14
91B70670.1
92D70670.1
101B69180.1
102H69180.1
111C45670.14
112G45670.14
121D69020.11
122H69020.11
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 278 -
Rwork0.421 5641 -
obs--99.46 %

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