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- PDB-7t2b: Crystal structure of the 5F TCR in complex with HLA-DP4-Ply -

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Basic information

Entry
Database: PDB / ID: 7t2b
TitleCrystal structure of the 5F TCR in complex with HLA-DP4-Ply
Components
  • (HLA class II histocompatibility antigen, DP ...) x 2
  • (T cell receptor, 5F, ...) 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: 2.8 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

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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
K: HLA class II histocompatibility antigen, DP alpha 1 chain
L: HLA class II histocompatibility antigen, DP beta 1 chain
M: Pneumolysin-derived peptide
P: HLA class II histocompatibility antigen, DP alpha 1 chain
Q: HLA class II histocompatibility antigen, DP beta 1 chain
R: Pneumolysin-derived peptide
D: T cell receptor, 5F, alpha chain
E: T cell receptor, 5F, beta chain
I: T cell receptor, 5F, alpha chain
J: T cell receptor, 5F, beta chain
N: T cell receptor, 5F, alpha chain
O: T cell receptor, 5F, beta chain
S: T cell receptor, 5F, alpha chain
T: T cell receptor, 5F, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,31940
Polymers378,71820
Non-polymers3,60120
Water18010
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, 5F, alpha chain
E: T cell receptor, 5F, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,73211
Polymers94,6795
Non-polymers1,0536
Water362
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, 5F, alpha chain
J: T cell receptor, 5F, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,67010
Polymers94,6795
Non-polymers9915
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, 5F, alpha chain
O: T cell receptor, 5F, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2469
Polymers94,6795
Non-polymers5674
Water181
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, 5F, alpha chain
T: T cell receptor, 5F, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,67010
Polymers94,6795
Non-polymers9915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.050, 110.780, 403.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 22074.725 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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Protein/peptide , 1 types, 4 molecules CHMR

#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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T cell receptor, 5F, ... , 2 types, 8 molecules DINSEJOT

#4: Protein
T cell receptor, 5F, alpha chain


Mass: 22814.195 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, 5F, beta chain


Mass: 27021.178 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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Sugars , 2 types, 11 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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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Non-polymers , 2 types, 19 molecules

#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Tacsimate pH 8, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.8→48.83 Å / Num. obs: 118241 / % possible obs: 99.6 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11691 / CC1/2: 0.776

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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, 6CUH

4p5k

6cuh


Resolution: 2.8→48.83 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 1990 1.69 %
Rwork0.2158 116063 -
obs0.2163 118053 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.49 Å2 / Biso mean: 72.8446 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.8→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25980 0 232 10 26222
Biso mean--96.73 53.25 -
Num. residues----3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226950
X-RAY DIFFRACTIONf_angle_d0.50336621
X-RAY DIFFRACTIONf_dihedral_angle_d17.2349778
X-RAY DIFFRACTIONf_chiral_restr0.0423958
X-RAY DIFFRACTIONf_plane_restr0.0034798
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.870.35481420.31818128100
2.87-2.950.38151510.31098220100
2.95-3.040.35121350.30358204100
3.04-3.140.33441360.30638239100
3.14-3.250.30071470.27698216100
3.25-3.380.27511350.25178239100
3.38-3.530.26881420.2389817999
3.53-3.720.25591450.22828278100
3.72-3.950.27061430.21468310100
3.95-4.260.241450.19258275100
4.26-4.680.21321370.16748299100
4.68-5.360.20541480.1696832599
5.36-6.750.23241400.19678459100
6.75-48.830.1881440.1914869299
Refinement TLS params.Method: refined / Origin x: -1.095 Å / Origin y: -27.7449 Å / Origin z: 50.2536 Å
111213212223313233
T0.462 Å2-0.0036 Å2-0.0306 Å2-0.6825 Å2-0.0241 Å2--0.3957 Å2
L0.1031 °20.0047 °2-0.0112 °2-0.1598 °2-0.0724 °2--0.084 °2
S0.048 Å °-0.0429 Å °0.0018 Å °0.0925 Å °-0.051 Å °-0.0345 Å °-0.0154 Å °0.0713 Å °0.0055 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 180
2X-RAY DIFFRACTION1allA181 - 184
3X-RAY DIFFRACTION1allB-1 - 188
4X-RAY DIFFRACTION1allB189
5X-RAY DIFFRACTION1allC-2 - 11
6X-RAY DIFFRACTION1allF1 - 180
7X-RAY DIFFRACTION1allF181 - 184
8X-RAY DIFFRACTION1allG2 - 188
9X-RAY DIFFRACTION1allG190
10X-RAY DIFFRACTION1allH-2 - 11
11X-RAY DIFFRACTION1allK1 - 180
12X-RAY DIFFRACTION1allK181 - 182
13X-RAY DIFFRACTION1allL2 - 189
14X-RAY DIFFRACTION1allM-1 - 11
15X-RAY DIFFRACTION1allP1 - 180
16X-RAY DIFFRACTION1allP181 - 184
17X-RAY DIFFRACTION1allQ-1 - 190
18X-RAY DIFFRACTION1allR-2 - 11
19X-RAY DIFFRACTION1allD9 - 219
20X-RAY DIFFRACTION1allD220
21X-RAY DIFFRACTION1allE3 - 257
22X-RAY DIFFRACTION1allE258
23X-RAY DIFFRACTION1allI8 - 219
24X-RAY DIFFRACTION1allJ3 - 257
25X-RAY DIFFRACTION1allJ258
26X-RAY DIFFRACTION1allN8 - 219
27X-RAY DIFFRACTION1allN220 - 221
28X-RAY DIFFRACTION1allO3 - 257
29X-RAY DIFFRACTION1allS8 - 219
30X-RAY DIFFRACTION1allS220
31X-RAY DIFFRACTION1allT3 - 257
32X-RAY DIFFRACTION1allU1 - 10

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