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- PDB-7t2c: Crystal structure of the B5 TCR in complex with HLA-DP4-Ply -

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Basic information

Entry
Database: PDB / ID: 7t2c
TitleCrystal structure of the B5 TCR in complex with HLA-DP4-Ply
Components
  • (HLA class II histocompatibility antigen, DP ...) x 2
  • (T cell receptor, B5, ...) 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 / PD-1 signaling / 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 / PD-1 signaling / positive regulation of T cell proliferation / 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 / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of type II interferon production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / 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 ...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
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: 3.1 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 1.3Oct 23, 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
D: T cell receptor, B5, alpha chain
E: T cell receptor, B5, beta chain
A: HLA class II histocompatibility antigen, DP alpha 1 chain
B: HLA class II histocompatibility antigen, DP beta 1 chain
C: Pneumolysin-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8988
Polymers95,1905
Non-polymers7083
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15370 Å2
ΔGint-61 kcal/mol
Surface area37240 Å2
Unit cell
Length a, b, c (Å)91.933, 77.712, 153.684
Angle α, β, γ (deg.)90.000, 96.710, 90.000
Int Tables number5
Space group name H-MI121

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Components

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T cell receptor, B5, ... , 2 types, 2 molecules DE

#1: Protein T cell receptor, B5, alpha chain


Mass: 22664.125 Da / Num. of mol.: 1
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
#2: Protein T cell receptor, B5, beta chain


Mass: 27840.002 Da / Num. of mol.: 1
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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HLA class II histocompatibility antigen, DP ... , 2 types, 2 molecules AB

#3: Protein HLA class II histocompatibility antigen, DP alpha 1 chain / T cell receptor alpha chain constant / DP(W3) / DP(W4) / HLA-SB alpha chain / MHC class II DP3- ...T cell receptor alpha chain constant / DP(W3) / DP(W4) / HLA-SB alpha chain / MHC class II DP3-alpha / MHC class II DPA1


Mass: 20943.336 Da / Num. of mol.: 1
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
#4: Protein HLA class II histocompatibility antigen, DP beta 1 chain / T cell receptor beta constant 1 / HLA class II histocompatibility antigen / DP(W4) beta chain / MHC ...T cell receptor beta constant 1 / HLA class II histocompatibility antigen / DP(W4) beta chain / MHC class II antigen DPB1


Mass: 21916.570 Da / Num. of mol.: 1
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, 1 molecules C

#5: Protein/peptide Pneumolysin-derived peptide


Mass: 1825.995 Da / Num. of mol.: 1
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 , 2 types, 2 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.: 1
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
#8: 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: 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, 4 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Calcium acetate, PEG 3350, Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.1→46.8 Å / Num. obs: 19670 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.985 / Net I/σ(I): 6.8
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1953 / CC1/2: 0.622

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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, 4OZI

4p5k

4ozi


Resolution: 3.1→46.8 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 983 5 %
Rwork0.2108 18667 -
obs0.2131 19650 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.73 Å2 / Biso mean: 69.983 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.1→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 46 3 6477
Biso mean--100.8 47.13 -
Num. residues----801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026659
X-RAY DIFFRACTIONf_angle_d0.4479062
X-RAY DIFFRACTIONf_dihedral_angle_d13.4672396
X-RAY DIFFRACTIONf_chiral_restr0.041986
X-RAY DIFFRACTIONf_plane_restr0.0031181
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.260.34461400.29962661100
3.26-3.470.33121380.26622613100
3.47-3.740.30421400.24332656100
3.74-4.110.24721390.20642664100
4.11-4.710.23141410.16962662100
4.71-5.930.21611420.17882684100
5.93-46.80.23681430.2055272799
Refinement TLS params.Method: refined / Origin x: 11.0047 Å / Origin y: -30.1096 Å / Origin z: -46.4767 Å
111213212223313233
T0.5339 Å2-0.016 Å2-0.1591 Å2-0.3569 Å2-0.0212 Å2--0.5878 Å2
L2.6628 °20.1338 °2-0.5151 °2-0.1843 °2-0.1424 °2--0.5144 °2
S0.1604 Å °0.1058 Å °-0.2339 Å °0.1154 Å °-0.0633 Å °-0.0708 Å °-0.0083 Å °0.0577 Å °-0.0988 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD2 - 204
2X-RAY DIFFRACTION1allE2 - 257
3X-RAY DIFFRACTION1allE258
4X-RAY DIFFRACTION1allA1 - 180
5X-RAY DIFFRACTION1allA181 - 182
6X-RAY DIFFRACTION1allB3 - 188
7X-RAY DIFFRACTION1allB189
8X-RAY DIFFRACTION1allC-1 - 10
9X-RAY DIFFRACTION1allF1 - 3

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