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- PDB-6dfw: TCR 8F10 in complex with IAg7-p8G9E -

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Basic information

Entry
Database: PDB / ID: 6dfw
TitleTCR 8F10 in complex with IAg7-p8G9E
Components
  • 8F10 alpha chain
  • 8F10 beta chain
  • H-2 class II histocompatibility antigen, A-D alpha chain
  • H2-Ab1 protein
KeywordsIMMUNE SYSTEM / T cell receptor / Type 1 Diabetes / Autoimmunity
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / adaptive immune response / early endosome / lysosome ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / adaptive immune response / early endosome / lysosome / external side of plasma membrane / cell surface / Golgi apparatus / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-D alpha chain / H2-Ab1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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 1.1Nov 6, 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
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: H2-Ab1 protein
E: 8F10 alpha chain
F: 8F10 beta chain
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: H2-Ab1 protein
G: 8F10 alpha chain
H: 8F10 beta chain


Theoretical massNumber of molelcules
Total (without water)192,9678
Polymers192,9678
Non-polymers00
Water00
1
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: H2-Ab1 protein
E: 8F10 alpha chain
F: 8F10 beta chain


Theoretical massNumber of molelcules
Total (without water)96,4834
Polymers96,4834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: H2-Ab1 protein
G: 8F10 alpha chain
H: 8F10 beta chain


Theoretical massNumber of molelcules
Total (without water)96,4834
Polymers96,4834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.094, 102.044, 136.001
Angle α, β, γ (deg.)90.00, 107.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23G
14F
24H

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
11ASPASPPROPROAA1 - 1821 - 182
21ASPASPPROPROCE1 - 1821 - 182
12LEULEUTRPTRPBB-27 - 1882 - 212
22LEULEUTRPTRPDF-27 - 1882 - 212
13GLUGLUTRPTRPEC2 - 1812 - 181
23GLUGLUGLNGLNGG2 - 1522 - 152
14ALAALAGLYGLYFD2 - 2382 - 238
24ALAALAGLYGLYHH2 - 2382 - 238

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 20907.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04228
#2: Protein H2-Ab1 protein


Mass: 25290.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31135
#3: Protein 8F10 alpha chain


Mass: 23405.010 Da / Num. of mol.: 2
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
#4: Protein 8F10 beta chain


Mass: 26880.781 Da / Num. of mol.: 2
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
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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 3350, 100mM formate pH7.0

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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: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 38891 / % possible obs: 96.9 % / Redundancy: 3.4 % / Net I/σ(I): 7.6
Reflection shellResolution: 3.2→3.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.2→50.01 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / SU B: 97.35 / SU ML: 0.69 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29691 1981 5.1 %RANDOM
Rwork0.23282 ---
obs0.23619 36910 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 132.243 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å2-0 Å20.7 Å2
2---6.28 Å20 Å2
3---2.66 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12189 0 0 0 12189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01912545
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.93417050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.26851522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06623.955617
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.539151975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2321577
X-RAY DIFFRACTIONr_chiral_restr0.1370.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219677
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_it1.0713.2956139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8244.9377641
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0663.3366406
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.73327.60818104
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A4260.12
12C4260.12
21B4440.11
22D4440.11
31E3060.12
32G3060.12
41F5520.02
42H5520.02
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 145 -
Rwork0.353 2683 -
obs--96.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7039-0.5331-0.28665.08011.72382.8908-0.1276-0.0303-0.15040.02830.1827-0.00250.03720.1692-0.05520.95510.00840.040.02980.11660.786820.4541-32.8573-57.0038
23.2336-1.3915-0.26844.24211.07161.8239-0.316-0.6611-0.56920.77160.4337-0.36680.29890.1953-0.11771.21850.0962-0.04760.14840.10990.850527.8549-40.3598-45.0891
34.6201-1.4964-2.23181.25431.06252.0408-0.2649-0.8697-0.00570.34480.06510.0570.4409-0.44250.19982.00690.24560.21311.20080.21270.9287-6.3433-17.6477-15.453
42.34290.1896-0.03470.9518-0.59651.8313-0.3006-0.42440.13710.2086-0.13810.6392-0.1582-0.89640.43871.98880.26920.28921.1235-0.17331.4987-17.5033-2.9439-27.0783
52.945-1.06230.42534.8628-2.34913.6476-0.0922-0.17410.3593-0.02470.0048-0.061-0.15-0.20940.08730.9656-0.0032-0.05180.041-0.12830.9414-25.6484-53.3829-56.8705
63.938-1.94890.86284.2362-1.28471.7838-0.3799-0.79830.72340.79280.40410.1332-0.4037-0.2355-0.02421.29370.11460.03750.1666-0.17811.0404-33.3826-46.1731-44.9161
72.7002-2.00912.49632.9151-2.73853.3607-0.2711-0.31580.15520.4205-0.1081-0.1304-0.59240.51540.37921.97210.1837-0.07371.2576-0.24130.95843.4962-72.547-11.9286
81.7672-1.06720.48522.16820.33241.4002-0.18090.00050.35850.1713-0.1659-0.60860.14840.87070.34681.87270.3111-0.11541.10670.03941.030810.6356-84.382-26.5077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION2B-27 - 189
3X-RAY DIFFRACTION3E2 - 182
4X-RAY DIFFRACTION4F2 - 238
5X-RAY DIFFRACTION5C1 - 182
6X-RAY DIFFRACTION6D-27 - 188
7X-RAY DIFFRACTION7G2 - 204
8X-RAY DIFFRACTION8H2 - 239

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