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- PDB-3pl6: Structure of Autoimmune TCR Hy.1B11 in complex with HLA-DQ1 and M... -

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Basic information

Entry
Database: PDB / ID: 3pl6
TitleStructure of Autoimmune TCR Hy.1B11 in complex with HLA-DQ1 and MBP 85-99
Components
  • (MHC class II HLA-DQ- ...) x 2
  • MBP peptide / T-cell receptor beta chain chimera
  • T-cell receptor alpha chain
KeywordsIMMUNE SYSTEM / TCR-MHC complex / Immunoglobulin fold / Immune receptor / Membrane
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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II antigen / HLA class II histocompatibility antigen DQ alpha chain / : / 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: 2.55 Å
AuthorsSethi, D.K. / Wucherpfennig, K.W.
CitationJournal: J.Exp.Med. / Year: 2011
Title: A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC.
Authors: Sethi, D.K. / Schubert, D.A. / Anders, A.K. / Heroux, A. / Bonsor, D.A. / Thomas, C.P. / Sundberg, E.J. / Pyrdol, J. / Wucherpfennig, K.W.
History
DepositionNov 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 HLA-DQ-beta chain
C: T-cell receptor alpha chain
D: MBP peptide / T-cell receptor beta chain chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3566
Polymers97,9144
Non-polymers4422
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-61 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.123, 124.815, 134.921
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 HLA-DQ- ... , 2 types, 2 molecules AB

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


Mass: 21960.480 Da / Num. of mol.: 1 / Fragment: UNP residues 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q30066, UniProt: A0A173ADG5*PLUS
#2: Protein MHC class II HLA-DQ-beta chain


Mass: 23447.137 Da / Num. of mol.: 1 / Fragment: UNP residues 31-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q67AJ6, UniProt: A0A0A8WFP6*PLUS

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Protein , 2 types, 2 molecules CD

#3: Protein T-cell receptor alpha chain


Mass: 22949.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein MBP peptide / T-cell receptor beta chain chimera


Mass: 29556.824 Da / Num. of mol.: 1 / Fragment: MBP (UNP residues 84-98)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: D3YTB3

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Sugars / Non-polymers , 2 types, 95 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Fragment: UNP residues 84-98
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.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCHAIN D IS CHIMERIC: MBP PEPTIDE IS CONNECTED TO THE N-TERMINUS OF T-CELL RECEPTOR BETA CHAIN VIA ...CHAIN D IS CHIMERIC: MBP PEPTIDE IS CONNECTED TO THE N-TERMINUS OF T-CELL RECEPTOR BETA CHAIN VIA AN ENGINEERED LINKER

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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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1 M ammonium sulfate, 12% PEG8000, 0.05 M sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2009
RadiationMonochromator: Cryogenically cooled double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 40993 / Num. obs: 40822 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.55→2.59 Å / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
CNS1.3refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→42 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 2045 5 %random
Rwork0.232 38776 --
obs-40821 99.6 %-
Solvent computationBsol: 37.0662 Å2
Displacement parametersBiso max: 114.7 Å2 / Biso mean: 57.7182 Å2 / Biso min: 29.69 Å2
Baniso -1Baniso -2Baniso -3
1-2.784 Å20 Å20 Å2
2--19.712 Å20 Å2
3----22.496 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.55→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 28 93 6526
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.503
X-RAY DIFFRACTIONc_mcbond_it1.4241.5
X-RAY DIFFRACTIONc_scbond_it1.9582
X-RAY DIFFRACTIONc_mcangle_it2.4892
X-RAY DIFFRACTIONc_scangle_it2.9982.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.640.39031800.35623771395198.1
2.64-2.750.3731970.3293829402699.9
2.75-2.870.37012190.313438254044100
2.87-3.020.34472170.29033821403899.9
3.02-3.210.30371880.27623902409099.9
3.21-3.460.2752390.24413817405699.9
3.46-3.810.28982040.24133878408299.9
3.81-4.360.24052020.20753912411499.9
4.36-5.490.18891980.17773952415099.8
5.49-420.20982010.21294069427098.6

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