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- PDB-5ksb: T15-DQ8.5-glia-gamma1 complex -

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Basic information

Entry
Database: PDB / ID: 5ksb
TitleT15-DQ8.5-glia-gamma1 complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • DQ8.5-glia-gamma1 peptide
  • T15 TCR alpha TRAV20*02
  • T15 TCR beta TRBV9*01
KeywordsIMMUNE SYSTEM / Celiac Disease T cell receptor peptide MHC complex
Function / homology
Function and homology information


nutrient reservoir activity / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / MHC class II antigen presentation ...nutrient reservoir activity / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / cell surface receptor signaling pathway / endosome membrane / immune response / lysosomal membrane / Golgi membrane / membrane / plasma membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / 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
T cell receptor alpha variable 20 / T cell receptor beta variable 9 / MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain / Gamma-gliadin
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsPetersen, J. / Rossjohn, J. / Reid, H.H.
CitationJournal: Structure / Year: 2016
Title: Diverse T Cell Receptor Gene Usage in HLA-DQ8-Associated Celiac Disease Converges into a Consensus Binding Solution.
Authors: Petersen, J. / Kooy-Winkelaar, Y. / Loh, K.L. / Tran, M. / van Bergen, J. / Koning, F. / Rossjohn, J. / Reid, H.H.
History
DepositionJul 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / diffrn_source / 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 / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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 / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: T15 TCR alpha TRAV20*02
F: T15 TCR beta TRBV9*01
G: T15 TCR alpha TRAV20*02
H: T15 TCR beta TRBV9*01
I: DQ8.5-glia-gamma1 peptide
J: DQ8.5-glia-gamma1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,42616
Polymers197,69310
Non-polymers1,7346
Water2,936163
1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
G: T15 TCR alpha TRAV20*02
H: T15 TCR beta TRBV9*01
J: DQ8.5-glia-gamma1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7138
Polymers98,8465
Non-polymers8673
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-54 kcal/mol
Surface area37490 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: T15 TCR alpha TRAV20*02
F: T15 TCR beta TRBV9*01
I: DQ8.5-glia-gamma1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7138
Polymers98,8465
Non-polymers8673
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-53 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.890, 125.050, 165.630
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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HLA class II histocompatibility antigen, DQ ... , 2 types, 4 molecules ACBD

#1: Protein HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


Mass: 21501.840 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: P01909
#2: Protein HLA class II histocompatibility antigen, DQ beta 1 chain


Mass: 25827.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat), (gene. exp.) Homo sapiens (human)
Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19707, UniProt: P08079*PLUS

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Protein , 2 types, 4 molecules EGFH

#3: Protein T15 TCR alpha TRAV20*02


Mass: 22878.301 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) / References: UniProt: A0A0B4J274*PLUS
#4: Protein T15 TCR beta TRBV9*01


Mass: 27421.457 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) / References: UniProt: A0A580*PLUS

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Protein/peptide / Non-polymers , 2 types, 165 molecules IJ

#5: Protein/peptide DQ8.5-glia-gamma1 peptide


Mass: 1217.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P08079*PLUS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 6 molecules

#6: 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.: 2 / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 8% Tacsimate pH 7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→85 Å / Num. obs: 53672 / % possible obs: 99.38 % / Redundancy: 2 % / Biso Wilson estimate: 56.06 Å2 / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.9→85 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.9 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 2.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.716 / SU Rfree Blow DPI: 0.356 / SU Rfree Cruickshank DPI: 0.364
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2710 5.05 %RANDOM
Rwork0.219 ---
obs0.221 53672 99.4 %-
Displacement parametersBiso mean: 55.31 Å2
Baniso -1Baniso -2Baniso -3
1-7.464 Å20 Å20 Å2
2--12.8039 Å20 Å2
3----20.2679 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.9→85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12831 0 112 163 13106
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813301HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9918151HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5980SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes342HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1929HARMONIC5
X-RAY DIFFRACTIONt_it13301HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion3.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1743SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14156SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 195 5.03 %
Rwork0.259 3679 -
all0.263 3874 -
obs--98.52 %
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)
12.01040.5769-0.59291.025-0.09942.60120.0811-0.5683-0.11040.4373-0.16990.24920.0353-0.06250.08880.0709-0.19230.09280.0176-0.0378-0.1299-62.5723-21.407830.9544
23.2980.8546-0.29622.0119-0.3931.5030.0751-0.085-0.01340.0747-0.04460.4271-0.1144-0.2862-0.0306-0.1629-0.04290.0862-0.2073-0.08770.1443-72.7309-17.063317.441
31.35490.4310.33412.1550.19841.62320.0498-0.47950.10330.4449-0.135-0.0814-0.05580.08850.0852-0.069-0.135-0.0387-0.103-0.00410.16131.377821.378731.0431
43.15840.20090.19561.669-0.08051.32310.0419-0.12770.05920.1045-0.0967-0.51830.07180.16950.0548-0.1782-0.0495-0.0785-0.24670.04220.218311.524317.080917.5132
53.20840.21141.86650.8377-0.35051.09050.12780.14710.1829-0.1705-0.13120.0223-0.0090.09010.0034-0.03760.14170.0114-0.1112-0.07480.1439-38.493113.4181-14.1787
62.11780.00140.68991.9154-0.22661.05820.1065-0.08480.15670.0257-0.11960.3528-0.17550.02280.0131-0.15350.00770.1089-0.2869-0.05170.1775-48.957110.79142.438
73.64980.2781-1.89990.86950.41930.80280.08890.2422-0.0875-0.1676-0.0894-0.06120.0637-0.11950.00050.04960.14820.0372-0.0320.0815-0.0231-22.7213-13.4687-14.0802
82.53810.1398-0.89461.51180.00861.22070.0798-0.214-0.00470.0134-0.1343-0.28680.25830.12410.0546-0.08820.0006-0.054-0.25570.02250.1162-12.2042-10.7382.5088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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