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- PDB-8vd2: Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1 -

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Basic information

Entry
Database: PDB / ID: 8vd2
TitleHuman TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1
Components
  • (MHC class II HLA-DQ- ...) x 2
  • (T-CELL-RECEPTOR, TCR ET650-4 ...) x 2
  • Hybrid insulin peptide (HIP; InsC8-15-IAPP23-29 )
KeywordsIMMUNE SYSTEM / Immune T cell receptor-pMHC II complex
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
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 ...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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class II HLA-DQ-beta-1 / MHC class II HLA-DQ-alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTran, T.M. / Lim, J.J. / Loh, T.Y. / Mannering, I.S. / Rossjohn, J. / Reid, H.H.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1123586 Australia
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8.
Authors: Tran, M.T. / Lim, J.J. / Loh, T.J. / Mannering, S.I. / Rossjohn, J. / Reid, H.H.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 9, 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-1
C: Hybrid insulin peptide (HIP; InsC8-15-IAPP23-29 )
D: T-CELL-RECEPTOR, TCR ET650-4 alpha
E: T-CELL-RECEPTOR, TCR ET650-4 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5266
Polymers95,3055
Non-polymers2211
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.121, 109.463, 109.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / DQA1*03:01 (DQ8-alpha chain


Mass: 21150.596 Da / Num. of mol.: 1 / Mutation: I75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Organ: Parenchyma / Plasmid: pZip3 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: Q30069
#2: Protein MHC class II HLA-DQ-beta-1 / DQB1*03:02 (DQ8-beta chain)


Mass: 22605.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Class II histocompatibility antigen, alpha domain / Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Plasmid: pZip3 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: O19707

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T-CELL-RECEPTOR, TCR ET650-4 ... , 2 types, 2 molecules DE

#4: Protein T-CELL-RECEPTOR, TCR ET650-4 alpha


Mass: 22921.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human CD4+ T cell clone isolated from PBMC of recent onset T1D patient
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV26-1*01 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli (E.coli)
#5: Protein T-CELL-RECEPTOR, TCR ET650-4 beta


Mass: 27153.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human CD4+ T cell clone isolated from PBMC of recent onset T1D patient
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV5-1*01 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli (E.coli)

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Protein/peptide / Sugars / Non-polymers , 3 types, 13 molecules C

#3: Protein/peptide Hybrid insulin peptide (HIP; InsC8-15-IAPP23-29 )


Mass: 1474.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A fusion of proinsulin C-peptide fragment and IAPP1 fragment
Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Organ: Pancreas / Details (production host): pZip3 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B
#6: 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.: 1 / Source method: obtained synthetically / 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M potassium dihydrogen phosphate (KH2PO4), 15% w/v PEG 20,000 with seeding and additive 30 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.9→49 Å / Num. obs: 20755 / % possible obs: 100 % / Redundancy: 3.1 % / Biso Wilson estimate: 58.91 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.096 / Rrim(I) all: 0.171 / Net I/σ(I): 7.8
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3281 / CC1/2: 0.817 / Rpim(I) all: 0.4 / Rrim(I) all: 0.718

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoXDSdata reduction
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49 Å / SU ML: 0.3925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 1057 5.11 %
Rwork0.2212 19648 -
obs0.2231 20705 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 14 11 6323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166472
X-RAY DIFFRACTIONf_angle_d0.44688826
X-RAY DIFFRACTIONf_chiral_restr0.0462983
X-RAY DIFFRACTIONf_plane_restr0.00381146
X-RAY DIFFRACTIONf_dihedral_angle_d12.08262294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.38761330.30462401X-RAY DIFFRACTION100
3.03-3.190.33221350.26832392X-RAY DIFFRACTION100
3.19-3.390.29171310.26522435X-RAY DIFFRACTION100
3.39-3.650.29691210.23122441X-RAY DIFFRACTION99.92
3.65-4.020.23991400.21122421X-RAY DIFFRACTION99.96
4.02-4.60.22391150.18462476X-RAY DIFFRACTION100
4.6-5.80.20461320.18942501X-RAY DIFFRACTION99.92
5.8-490.26051500.22422581X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.859894162 Å / Origin y: -19.748337874 Å / Origin z: -19.5718002526 Å
111213212223313233
T0.409500712391 Å20.0439214455624 Å20.0198615960935 Å2-0.367290972303 Å20.0729072689516 Å2--0.311761571532 Å2
L2.14177484966 °2-0.882331688473 °2-1.33510307662 °2-0.758244581076 °20.657798734002 °2--0.829217217711 °2
S0.147772650552 Å °0.159172631093 Å °0.121747625228 Å °-0.07754781969 Å °-0.0589934639106 Å °-0.0432281830138 Å °-0.159482275849 Å °-0.10895554147 Å °-0.0823870009465 Å °
Refinement TLS groupSelection details: all

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