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- PDB-6dfx: human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide -

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Basic information

Entry
Database: PDB / ID: 6dfx
Titlehuman diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide
Components
  • (MHC class II ...) x 2
  • T1D3 alpha chain
  • T1D3 beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / type 1 diabetes / autoimmunity
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II HLA-DQ-alpha chain / HLA class II histocompatibility antigen DQ beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II antigen
D: MHC class II HLA-DQ-alpha chain
E: MHC class II antigen
G: T1D3 alpha chain
H: T1D3 beta chain
I: T1D3 alpha chain
J: T1D3 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,19611
Polymers192,4888
Non-polymers7083
Water13,962775
1
A: MHC class II HLA-DQ-alpha chain
B: MHC class II antigen
G: T1D3 alpha chain
H: T1D3 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7316
Polymers96,2444
Non-polymers4862
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class II HLA-DQ-alpha chain
E: MHC class II antigen
I: T1D3 alpha chain
J: T1D3 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4655
Polymers96,2444
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.705, 88.896, 116.777
Angle α, β, γ (deg.)90.00, 104.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13G
23I
14H
24J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 179
2010D1 - 179
1020B-27 - 190
2020E-27 - 190
1030G8 - 201
2030I8 - 201
1040H3 - 245
2040J3 - 239

NCS ensembles :
ID
1
2
3
4

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Components

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MHC class II ... , 2 types, 4 molecules ADBE

#1: Protein MHC class II HLA-DQ-alpha chain


Mass: 21373.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q30069
#2: Protein MHC class II antigen


Mass: 25119.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: U3PYM0

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Protein , 2 types, 4 molecules GIHJ

#3: Protein T1D3 alpha chain


Mass: 22907.236 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) / Strain (production host): BL21-Gold(DE3)pLysS AG
#4: Protein T1D3 beta chain


Mass: 26843.746 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) / Strain (production host): BL21-Gold(DE3)pLysS AG

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Sugars , 2 types, 2 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 776 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000, 100mM cacodylate pH6.2, 400mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 142449 / % possible obs: 98.1 % / Redundancy: 4.5 % / Net I/σ(I): 14.4
Reflection shellResolution: 2.03→2.2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.03→50.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 11.433 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21657 7241 5.1 %RANDOM
Rwork0.18083 ---
obs0.18273 135207 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å21.09 Å2
2--0.5 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.03→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12872 0 46 775 13693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.01913250
X-RAY DIFFRACTIONr_bond_other_d0.0090.0212071
X-RAY DIFFRACTIONr_angle_refined_deg2.4931.93718011
X-RAY DIFFRACTIONr_angle_other_deg1.796327753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.28451601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42424660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.622152119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3461591
X-RAY DIFFRACTIONr_chiral_restr0.1580.21965
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02115109
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023232
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_it2.142.9186446
X-RAY DIFFRACTIONr_mcbond_other2.142.9186445
X-RAY DIFFRACTIONr_mcangle_it3.1094.3668033
X-RAY DIFFRACTIONr_mcangle_other3.1094.3668034
X-RAY DIFFRACTIONr_scbond_it2.9613.2186804
X-RAY DIFFRACTIONr_scbond_other2.963.2186804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4124.79979
X-RAY DIFFRACTIONr_long_range_B_refined5.8923.59314511
X-RAY DIFFRACTIONr_long_range_B_other5.8923.59614512
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)
11A190200.12
12D190200.12
21B206180.14
22E206180.14
31G175420.18
32I175420.18
41H242140.16
42J242140.16
LS refinement shellResolution: 2.028→2.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 489 -
Rwork0.314 9807 -
obs--97.76 %
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)
11.4565-0.3894-0.64751.39770.74011.95370.00480.2972-0.2413-0.2067-0.06240.05060.1918-0.08060.05760.09050.009-00.066-0.03670.0941233.34395.807119.6168
22.3547-0.7318-0.82071.21890.3651.40760.09090.18610.055-0.1246-0.0468-0.1278-0.09090.1537-0.04410.0162-0.00570.00540.06190.01610.0678245.239516.402422.4617
31.71520.3611-0.54961.0385-0.65371.8726-0.0175-0.1994-0.21590.14880.0207-0.03090.20380.0062-0.00320.09220.03930.01050.14220.04990.1479292.38138.172533.8303
42.410.6772-0.63430.8538-0.18980.97670.0749-0.12090.17240.0909-0.00370.0789-0.0671-0.0706-0.07120.03820.0515-0.0060.12710.02050.1419281.898920.108131.4222
50.80950.1254-1.04110.1625-0.1943.4747-0.0103-0.4725-0.08810.1833-0.052-0.04370.12340.31360.06230.25130.0073-0.02510.3375-0.00490.2029225.363218.124875.8136
61.0693-0.0269-1.14610.2281-0.07191.7024-0.0646-0.1655-0.01920.11510.0239-0.02420.05040.12780.04080.07810.00360.00130.07460.01280.1702207.656211.369669.8418
70.54510.1607-1.11440.1021-0.21773.6169-0.11210.225-0.0859-0.14150.0870.04160.1445-0.33620.02510.2982-0.013-0.06710.28670.06420.3204302.191922.7326-20.9695
80.44880.1267-0.6750.626-0.82491.9505-0.0563-0.0341-0.1031-0.24360.07190.01720.2481-0.0441-0.01570.1401-0.0388-0.00530.10130.00070.1886319.512415.3837-15.5659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 179
2X-RAY DIFFRACTION2B-27 - 344
3X-RAY DIFFRACTION3D1 - 179
4X-RAY DIFFRACTION4E-27 - 190
5X-RAY DIFFRACTION5G8 - 201
6X-RAY DIFFRACTION6H3 - 431
7X-RAY DIFFRACTION7I8 - 201
8X-RAY DIFFRACTION8J3 - 398

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