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- PDB-7t2d: Crystal structure of the B1 TCR in complex with HLA-DP4-Ply -

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Basic information

Entry
Database: PDB / ID: 7t2d
TitleCrystal structure of the B1 TCR in complex with HLA-DP4-Ply
Components
  • (HLA class II histocompatibility antigen, DP ...) x 2
  • (T cell receptor, B1, ...) x 2
  • Pneumolysin-derived peptide
KeywordsIMMUNE SYSTEM / TCR-pHLA complex
Function / homology
Function and homology information


MHC class II receptor activity / alpha-beta T cell receptor complex / cholesterol binding / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / positive regulation of T cell proliferation ...MHC class II receptor activity / alpha-beta T cell receptor complex / cholesterol binding / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / response to bacterium / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / cellular response to type II interferon / positive regulation of T cell activation / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity / killing of cells of another organism / adaptive immune response / immune response / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / host cell plasma membrane / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) ...Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / T-cell receptor alpha chain, constant domain / 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 / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen, DP alpha 1 chain / Pneumolysin
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCiacchi, L. / Farenc, C. / Petersen, J. / Reid, H.H. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Immunity / Year: 2023
Title: CD4 + T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity.
Authors: Ciacchi, L. / van de Garde, M.D.B. / Ladell, K. / Farenc, C. / Poelen, M.C.M. / Miners, K.L. / Llerena, C. / Reid, H.H. / Petersen, J. / Price, D.A. / Rossjohn, J. / van Els, C.A.C.M.
History
DepositionDec 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 13, 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: HLA class II histocompatibility antigen, DP alpha 1 chain
B: HLA class II histocompatibility antigen, DP beta 1 chain
C: Pneumolysin-derived peptide
F: HLA class II histocompatibility antigen, DP alpha 1 chain
G: HLA class II histocompatibility antigen, DP beta 1 chain
H: Pneumolysin-derived peptide
D: T cell receptor, B1, alpha chain
E: T cell receptor, B1, beta chain
I: T cell receptor, B1, alpha chain
J: T cell receptor, B1, beta chain
K: HLA class II histocompatibility antigen, DP alpha 1 chain
L: HLA class II histocompatibility antigen, DP beta 1 chain
M: Pneumolysin-derived peptide
N: T cell receptor, B1, alpha chain
O: T cell receptor, B1, beta chain
P: HLA class II histocompatibility antigen, DP alpha 1 chain
Q: HLA class II histocompatibility antigen, DP beta 1 chain
R: Pneumolysin-derived peptide
S: T cell receptor, B1, alpha chain
T: T cell receptor, B1, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,01032
Polymers380,57020
Non-polymers4,44012
Water1267
1
A: HLA class II histocompatibility antigen, DP alpha 1 chain
B: HLA class II histocompatibility antigen, DP beta 1 chain
C: Pneumolysin-derived peptide
D: T cell receptor, B1, alpha chain
E: T cell receptor, B1, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3348
Polymers95,1435
Non-polymers1,1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class II histocompatibility antigen, DP alpha 1 chain
G: HLA class II histocompatibility antigen, DP beta 1 chain
H: Pneumolysin-derived peptide
I: T cell receptor, B1, alpha chain
J: T cell receptor, B1, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3348
Polymers95,1435
Non-polymers1,1913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA class II histocompatibility antigen, DP alpha 1 chain
L: HLA class II histocompatibility antigen, DP beta 1 chain
M: Pneumolysin-derived peptide
N: T cell receptor, B1, alpha chain
O: T cell receptor, B1, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1728
Polymers95,1435
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: HLA class II histocompatibility antigen, DP alpha 1 chain
Q: HLA class II histocompatibility antigen, DP beta 1 chain
R: Pneumolysin-derived peptide
S: T cell receptor, B1, alpha chain
T: T cell receptor, B1, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1728
Polymers95,1435
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.709, 193.570, 236.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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HLA class II histocompatibility antigen, DP ... , 2 types, 8 molecules AFKPBGLQ

#1: Protein
HLA class II histocompatibility antigen, DP alpha 1 chain / DP(W3) / DP(W4) / HLA-SB alpha chain / MHC class II DP3-alpha / MHC class II DPA1


Mass: 20943.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPA1, HLA-DP1A, HLASB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20036
#2: Protein
HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen / DP(W4) beta chain / MHC class II antigen DPB1


Mass: 21916.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPB1, HLA-DP1B / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04440

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T cell receptor, B1, ... , 2 types, 8 molecules DINSEJOT

#4: Protein
T cell receptor, B1, alpha chain


Mass: 23295.541 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01848
#5: Protein
T cell receptor, B1, beta chain


Mass: 27161.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01850

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Protein/peptide / Non-polymers , 2 types, 11 molecules CHMR

#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
#3: Protein/peptide
Pneumolysin-derived peptide


Mass: 1825.995 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ply, SPD_1726 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q04IN8

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Sugars , 4 types, 12 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: 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.: 8
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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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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: Potassium sodium tartrate, Tris-HCl pH 8

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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: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.4→33.4 Å / Num. obs: 101100 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.995 / Net I/σ(I): 5.6
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9986 / CC1/2: 0.691

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P5K, 4MAY

4p5k

4may


Resolution: 3.4→33.4 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 5020 4.98 %
Rwork0.2364 95794 -
obs0.2382 100814 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 248.98 Å2 / Biso mean: 103.2742 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.4→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25951 0 290 7 26248
Biso mean--152.41 57.57 -
Num. residues----3218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327077
X-RAY DIFFRACTIONf_angle_d0.50236856
X-RAY DIFFRACTIONf_dihedral_angle_d18.6399799
X-RAY DIFFRACTIONf_chiral_restr0.0434009
X-RAY DIFFRACTIONf_plane_restr0.0034826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.440.40451590.35913162100
3.44-3.480.4151340.35383180100
3.48-3.520.36081800.34713156100
3.52-3.570.37091610.32963159100
3.57-3.610.3391650.31563146100
3.61-3.660.34171580.30963192100
3.66-3.710.36051810.30243178100
3.71-3.770.36191750.29893149100
3.77-3.830.31291550.28993169100
3.83-3.890.37381710.26983184100
3.89-3.960.28191740.26113136100
3.96-4.030.27251810.24913186100
4.03-4.110.27911610.24573187100
4.11-4.190.26471580.23773172100
4.19-4.280.25941780.2287314599
4.28-4.380.24461560.21963201100
4.38-4.490.221820.20323182100
4.49-4.610.26111570.20033191100
4.61-4.750.21251550.1939319199
4.75-4.90.22391550.20023193100
4.9-5.070.23361380.20443216100
5.07-5.280.23941680.21123216100
5.28-5.520.26511860.21823188100
5.52-5.810.25522000.21953184100
5.81-6.170.29811700.23263233100
6.17-6.640.26551560.23123246100
6.64-7.30.27051610.21683239100
7.3-8.340.2072010.19893239100
8.34-10.460.18911780.18363300100
10.46-33.40.30841660.243327495
Refinement TLS params.Method: refined / Origin x: -39.9831 Å / Origin y: -17.5639 Å / Origin z: -59.2047 Å
111213212223313233
T0.7539 Å20.0456 Å2-0.0101 Å2-0.698 Å2-0.0672 Å2--0.7926 Å2
L0.0212 °20.0039 °20.0681 °2--0.0748 °2-0.0622 °2--0.1247 °2
S0.0185 Å °-0.0171 Å °0.0448 Å °-0.0034 Å °-0.0339 Å °0.0002 Å °-0.0015 Å °-0.0111 Å °0.007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 180
2X-RAY DIFFRACTION1allA181 - 185
3X-RAY DIFFRACTION1allB2 - 188
4X-RAY DIFFRACTION1allC-2 - 11
5X-RAY DIFFRACTION1allF1 - 180
6X-RAY DIFFRACTION1allF181 - 185
7X-RAY DIFFRACTION1allG2 - 187
8X-RAY DIFFRACTION1allG188
9X-RAY DIFFRACTION1allH-2 - 11
10X-RAY DIFFRACTION1allD1 - 216
11X-RAY DIFFRACTION1allE9 - 257
12X-RAY DIFFRACTION1allI1 - 216
13X-RAY DIFFRACTION1allJ7 - 257
14X-RAY DIFFRACTION1allK1 - 180
15X-RAY DIFFRACTION1allK181 - 184
16X-RAY DIFFRACTION1allL2 - 190
17X-RAY DIFFRACTION1allM-2 - 11
18X-RAY DIFFRACTION1allN1 - 214
19X-RAY DIFFRACTION1allO6 - 257
20X-RAY DIFFRACTION1allP1 - 180
21X-RAY DIFFRACTION1allP181 - 184
22X-RAY DIFFRACTION1allQ2 - 188
23X-RAY DIFFRACTION1allQ189
24X-RAY DIFFRACTION1allR-2 - 11
25X-RAY DIFFRACTION1allS1 - 214
26X-RAY DIFFRACTION1allT6 - 257
27X-RAY DIFFRACTION1allU1 - 7

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