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- PDB-5ks9: Bel502-DQ8-glia-alpha1 complex -

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Basic information

Entry
Database: PDB / ID: 5ks9
TitleBel502-DQ8-glia-alpha1 complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • Bel502 TCR alpha TRAV20*01
  • Bel502 TCR beta TRBV9*01
  • DQ8-glia-alpha1 peptide
KeywordsIMMUNE SYSTEM / Celiac Disease T cell receptor peptide MHC complex
Function / homology
Function and homology information


nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / T cell receptor complex / response to bacterium / MHC class II protein complex / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / 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 ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / 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 / HLA class II histocompatibility antigen DQ alpha chain / Alpha/beta-gliadin MM1 / HLA class II histocompatibility antigen DQ alpha chain / Alpha-gliadin / HLA class II histocompatibility antigen DQ beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPetersen, J. / Rossjohn, J. / Reid, H.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1085875 Australia
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 1.2Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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: Bel502 TCR alpha TRAV20*01
F: Bel502 TCR beta TRBV9*01
G: Bel502 TCR alpha TRAV20*01
H: Bel502 TCR beta TRBV9*01
I: DQ8-glia-alpha1 peptide
J: DQ8-glia-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,96218
Polymers199,91710
Non-polymers1,0458
Water12,466692
1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
G: Bel502 TCR alpha TRAV20*01
H: Bel502 TCR beta TRBV9*01
J: DQ8-glia-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4819
Polymers99,9595
Non-polymers5234
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: Bel502 TCR alpha TRAV20*01
F: Bel502 TCR beta TRBV9*01
I: DQ8-glia-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4819
Polymers99,9595
Non-polymers5234
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.560, 56.870, 232.050
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number4
Space group name H-MP1211

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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


Mass: 21882.221 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: Q30063, UniProt: L8E864*PLUS
#2: Protein HLA class II histocompatibility antigen, DQ beta 1 chain / MHC class II antigen DQB1


Mass: 26198.922 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: U3PYM0, UniProt: R9XSW3*PLUS

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Protein , 2 types, 4 molecules EGFH

#3: Protein Bel502 TCR alpha TRAV20*01


Mass: 22984.539 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 Bel502 TCR beta TRBV9*01


Mass: 27233.248 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 / Sugars , 2 types, 6 molecules IJ

#5: Protein/peptide DQ8-glia-alpha1 peptide


Mass: 1659.665 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: P18573*PLUS
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

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Non-polymers , 2 types, 696 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Na-Acetate, 22% PEG8000, Tris/Cl pH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.55→46.9 Å / Num. obs: 63405 / % possible obs: 98.84 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.28 Å2 / Net I/σ(I): 5.52

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.9 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.612 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.661 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1263 1.99 %RANDOM
Rwork0.199 ---
obs0.2 63405 98.8 %-
Displacement parametersBiso mean: 36.26 Å2
Baniso -1Baniso -2Baniso -3
1-5.1749 Å20 Å23.1259 Å2
2---4.8981 Å20 Å2
3----0.2768 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.55→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12756 0 60 694 13510
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01513168HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1617958HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5926SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes343HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1913HARMONIC5
X-RAY DIFFRACTIONt_it13168HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion3.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1708SEMIHARMONIC5
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_contact14623SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 102 2.18 %
Rwork0.216 4578 -
all0.217 4680 -
obs--99.15 %
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)
11.0467-0.08910.77280.6692-0.36491.5665-0.0815-0.16470.23470.1155-0.0588-0.0195-0.2794-0.1810.1403-0.0508-0.02870.00420.0255-0.028-0.12179.5003-19.975325.423
20.9836-0.19960.61920.50970.03411.8271-0.0412-0.2289-0.10270.15780.0470.05480.1082-0.1313-0.0058-0.0658-0.02090.04240.01720.0464-0.155514.575-35.221130.5446
32.0397-0.36310.48520.9392-0.22291.5248-0.1341-0.53580.42630.17880.0133-0.0516-0.3375-0.20860.1208-0.1436-0.02230.0125-0.1395-0.09420.101615.07285.9341-90.6624
42.315-0.27190.99980.639-0.22442.1846-0.0837-0.6276-0.1340.20150.10350.06860.0199-0.1676-0.0199-0.1793-0.02240.0524-0.12210.05-0.010919.8419-9.4393-87.8914
51.38040.2472-2.09170.5994-0.30944.5371-0.1873-0.0973-0.0563-0.16110.00450.01790.31920.41440.1828-0.13910.10590.0391-0.16560.00940.108442.2116-10.673-139.3006
60.7312-0.361-1.07830.0667-0.25751.44050.02790.2-0.0664-0.0419-0.02240.10040.0285-0.0701-0.0055-0.1148-0.02330.0064-0.0676-0.05710.108132.26484.7388-144.1905
71.3856-0.0397-2.46440.34420.33494.0528-0.1777-0.0553-0.1311-0.07230.03670.02410.32970.17050.141-0.0880.05050.01710.0155-0.0072-0.106436.6831-36.5916-23.0247
81.746-0.4648-1.82060.0113-0.29651.81080.03420.426-0.1045-0.010.00410.07270.0117-0.3487-0.0383-0.115-0.0461-0.01330.0898-0.0853-0.199526.6115-21.2168-28.1468
90.4542-1.8467-1.3435.1538-1.96752.09810.0232-0.0006-0.0547-0.0464-0.0881-0.0386-0.1040.04150.0649-0.2021-0.02460.0511-0.2908-0.00910.223220.337-4.1074-110.0395
100.5477-0.6101-2.49593.6388-1.17971.65570.00780.06370.0039-0.0061-0.0502-0.0919-0.042-0.03220.0423-0.05110.04070.0407-0.0369-0.0069-0.003214.7865-30.00386.0008
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|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }

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