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- PDB-4grl: Crystal structure of a autoimmune TCR-MHC complex -

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Basic information

Entry
Database: PDB / ID: 4grl
TitleCrystal structure of a autoimmune TCR-MHC complex
Components
  • (MHC class II ...) x 2
  • TCR Hy.1B11 alpha chain
  • TCR Hy.1B11 beta chain
KeywordsIMMUNE SYSTEM / immune complex / peptide antigen presentation / multiple sclerosis / 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 / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsSethi, D.K. / Wucherpfennig, K.W.
CitationJournal: Nat Commun / Year: 2013
Title: Crossreactivity of a human autoimmune TCR is dominated by a single TCR loop.
Authors: Sethi, D.K. / Gordo, S. / Schubert, D.A. / Wucherpfennig, K.W.
History
DepositionAug 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
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
C: TCR Hy.1B11 alpha chain
D: TCR Hy.1B11 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0205
Polymers96,7994
Non-polymers2211
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-70 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.011, 125.583, 134.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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MHC class II ... , 2 types, 2 molecules AB

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


Mass: 20762.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: alpha chain, HLA-DQ1, HLA-DQA1, MHC CLASS II MOLECULE / Plasmid: pEE13.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: Q30066
#2: Protein MHC class II antigen


Mass: 23232.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: beta chain, HLA-DQ1, HLA-DQB1, MHC CLASS II MOLECULE / Plasmid: pEE13.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: Q67AJ6

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Protein , 2 types, 2 molecules CD

#3: Protein TCR Hy.1B11 alpha chain


Mass: 23266.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCR Hy.1B11 alpha chain / Plasmid: pet22b / Production host: Escherichia coli (E. coli)
#4: Protein TCR Hy.1B11 beta chain


Mass: 29536.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCR Hy.1B11 beta chain / Plasmid: pet22b / Production host: Escherichia coli (E. coli)

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Sugars / Non-polymers , 2 types, 36 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 3-17 ARE A PEPTIDE FROM PSEUDOMONAS, COVALENTLY ATTACHED TO N-TERM OF TCR BETA CHAIN

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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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 295 K / Method: hanging drop vapor diffusion / pH: 6.1
Details: 0.1% Ammonium sulphate, 12% peg 6000, 0.1M Sodium citrate, pH 6.1, hanging drop vapor diffusion, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.86→50 Å / Num. all: 32941 / Num. obs: 29267 / % possible obs: 99.3 % / Observed criterion σ(I): 2.1 / Redundancy: 4 % / Rsym value: 0.081 / Net I/σ(I): 16.8
Reflection shellResolution: 2.86→2.96 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→36.601 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 1.35 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1432 4.96 %
Rwork0.2016 --
obs0.2044 28869 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.9383 Å2
Refinement stepCycle: LAST / Resolution: 2.86→36.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 14 35 6448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096583
X-RAY DIFFRACTIONf_angle_d1.2798950
X-RAY DIFFRACTIONf_dihedral_angle_d16.1962356
X-RAY DIFFRACTIONf_chiral_restr0.089977
X-RAY DIFFRACTIONf_plane_restr0.0051172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.96220.39471340.31222718X-RAY DIFFRACTION100
2.9622-3.08070.3871470.28872711X-RAY DIFFRACTION100
3.0807-3.22090.3481500.27392679X-RAY DIFFRACTION100
3.2209-3.39060.30471390.23912734X-RAY DIFFRACTION100
3.3906-3.60280.32861260.23422763X-RAY DIFFRACTION100
3.6028-3.88070.25711540.19492682X-RAY DIFFRACTION99
3.8807-4.27070.20861330.17582764X-RAY DIFFRACTION99
4.2707-4.88750.18681470.13872752X-RAY DIFFRACTION99
4.8875-6.15290.22461510.17812773X-RAY DIFFRACTION99
6.1529-36.60430.25161510.20632861X-RAY DIFFRACTION98
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)
12.33510.9709-0.57152.56042.13914.18670.03010.0987-0.0774-0.10940.1632-0.0888-0.22440.4421-0.14190.36450.0084-0.03370.1964-0.00290.27851.154310.369913.6416
20.58631.0719-0.11093.58530.04142.5473-0.04550.4061-0.0199-0.66690.2117-0.17370.25720.5232-0.20.4671-0.0455-0.07930.4691-0.07850.42036.100515.884417.6912
32.42241.59370.19581.79550.68884.0769-0.14640.8720.0954-0.63270.264-0.43180.44670.8636-0.09890.45290.00030.11540.6632-0.12490.41188.52685.274-2.7414
41.8355-0.15931.21612.19710.80742.59420.01820.6969-0.0928-0.70780.2029-0.49720.16761.2968-0.15740.7401-0.05210.10630.7489-0.17560.49698.90464.4463-4.6098
52.20380.1636-1.21142.26010.43293.28960.0153-0.2132-0.43810.63240.034-0.10770.41410.1849-0.0520.55790.0401-0.09030.3028-0.03210.3144-1.19611.869824.797
60.4527-0.031-0.04322.22431.07550.7458-0.4867-0.22360.2735-0.0647-0.21450.4655-0.2741-1.24990.53490.52820.134-0.01940.3686-0.03110.4274-11.864515.344318.2066
72.34890.87290.37094.5022-0.40834.4524-0.15820.50.1418-0.49340.16670.2181-0.5201-0.09580.06240.38770.0194-0.02680.41510.04130.2842-16.55261.3329-13.6442
82.40950.63890.71011.58330.61151.4833-0.29870.02780.1037-0.46320.20120.1946-0.6035-0.29650.2120.6156-0.008-0.11240.33450.08880.3453-15.64283.8568-14.4204
91.7984-0.5093-0.13870.95720.62760.39440.12760.33110.8089-1.16820.33670.2622-0.60280.4259-0.950.7791-0.00610.21590.4528-0.16160.6610.979244.603239.7623
102.4532-0.3002-0.6273.1611.51914.0226-0.0391-0.11180.0099-0.08710.02840.16920.1994-0.2739-0.05990.36410.0327-0.04340.3399-0.04290.42-3.115733.588941.5263
113.8658-0.08310.20092.22861.90771.68930.0049-0.08950.2439-0.4656-0.08860.3303-0.6929-0.12130.14530.41870.0439-0.06590.242-0.00040.4257-2.273235.463139.8171
125.20590.87343.3522.22490.96649.1753-0.5758-0.9588-1.2189-0.3348-0.14210.26140.0166-1.20320.18330.50770.07930.02440.0668-0.15760.63560.9548.120161.0037
134.6198-0.9730.38261.317-0.21941.09950.36270.05340.16190.4462-0.0916-0.99120.19631.6388-0.17850.33340.051-0.06720.6887-0.05890.477921.461549.947773.004
144.47221.8439-0.92425.9571-1.25685.023-0.10681.26590.4278-0.25610.15170.2118-0.65120.04640.03860.4150.0244-0.09480.47560.01420.308514.213354.786261.7051
153.65422.66621.79236.06350.96913.5039-0.97510.2933-0.4678-0.55940.47060.3193-0.3763-1.23490.18840.36870.0399-0.00240.543-0.03540.48688.257543.676168.3327
161.2742-2.1091-0.35463.3396-0.34785.44930.076-0.05260.82630.5450.0979-1.09070.05121.8029-0.75570.2339-0.4812-0.0918-0.1975-0.40570.916620.068960.090368.9227
173.46641.62910.64382.15610.86392.24480.1764-0.5697-0.8133-0.5558-0.3562-0.53160.1921.0903-0.17580.3026-0.0249-0.10490.8-0.05490.542224.267425.862443.6923
184.49560.84550.73871.9939-1.44071.57740.08790.35960.0358-0.40420.02860.12910.20920.1045-0.02990.41410.0035-0.02550.4281-0.13530.316214.525725.517633.928
191.8092-0.20451.34823.08890.63431.69930.13340.4049-0.1525-0.16760.2686-0.43320.07640.5328-0.3680.41260.0503-0.02010.5913-0.19370.421518.044324.686637.2324
201.6719-0.06631.68350.9504-0.13992.9515-0.71741.70320.3371-0.1350.3994-0.0853-1.17271.42780.40410.3727-0.1215-0.02941.036-0.23040.667431.704238.01247.2941
211.1870.07640.71721.3266-0.35571.2510.04820.3593-0.05210.14960.2394-0.15730.18010.0571-0.26040.2035-0.0448-0.03810.2947-0.07330.532419.473541.552368.946
223.76380.0755-0.08871.39620.32434.0902-0.08590.2992-0.154-0.00520.3316-0.01030.2827-0.2477-0.12250.22310.0344-0.04660.2189-0.09190.410819.517939.227465.7264
233.56390.0046-3.07891.773-0.21113.6314-0.28350.1394-0.4387-0.02090.0908-0.59810.10260.57360.36670.28040.0422-0.12030.665-0.15720.739233.387433.285260.6615
245.3933-2.08151.45053.3315-2.08362.7385-0.13410.70820.1554-0.3243-0.1556-0.54810.15880.38260.11540.47210.0162-0.0570.4208-0.11190.2947-0.294616.769924.7532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 97 )
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 191 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 14 )
10X-RAY DIFFRACTION10chain 'C' and (resid 15 through 61 )
11X-RAY DIFFRACTION11chain 'C' and (resid 62 through 105 )
12X-RAY DIFFRACTION12chain 'C' and (resid 106 through 119 )
13X-RAY DIFFRACTION13chain 'C' and (resid 120 through 138 )
14X-RAY DIFFRACTION14chain 'C' and (resid 139 through 161 )
15X-RAY DIFFRACTION15chain 'C' and (resid 162 through 178 )
16X-RAY DIFFRACTION16chain 'C' and (resid 179 through 192 )
17X-RAY DIFFRACTION17chain 'D' and (resid -2 through 21 )
18X-RAY DIFFRACTION18chain 'D' and (resid 22 through 62 )
19X-RAY DIFFRACTION19chain 'D' and (resid 63 through 104 )
20X-RAY DIFFRACTION20chain 'D' and (resid 105 through 119 )
21X-RAY DIFFRACTION21chain 'D' and (resid 120 through 157 )
22X-RAY DIFFRACTION22chain 'D' and (resid 158 through 210 )
23X-RAY DIFFRACTION23chain 'D' and (resid 211 through 240 )
24X-RAY DIFFRACTION24chain 'D' and (resid -24 through -11 )

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