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- PDB-7t2a: Crystal structure of HLA-DP4 in complex with Ply -

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Basic information

Entry
Database: PDB / ID: 7t2a
TitleCrystal structure of HLA-DP4 in complex with Ply
Components
  • HLA class II histocompatibility antigen, DP alpha 1 chain
  • HLA class II histocompatibility antigen, DP beta 1 chain
  • Pneumolysin-derived peptide
KeywordsIMMUNE SYSTEM / pHLA complex
Function / homology
Function and homology information


MHC class II receptor activity / transport vesicle membrane / cholesterol binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane ...MHC class II receptor activity / transport vesicle membrane / cholesterol binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / 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 / 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 / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / 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 / lysosomal membrane / Golgi 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 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta 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 / 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
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: 3.04 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

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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
D: HLA class II histocompatibility antigen, DP alpha 1 chain
E: HLA class II histocompatibility antigen, DP beta 1 chain
F: Pneumolysin-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25710
Polymers89,3726
Non-polymers8854
Water0
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1285
Polymers44,6863
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-34 kcal/mol
Surface area17860 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DP alpha 1 chain
E: HLA class II histocompatibility antigen, DP beta 1 chain
F: Pneumolysin-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1285
Polymers44,6863
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-30 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.669, 101.669, 215.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#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.: 2
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.: 2
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
#3: Protein/peptide Pneumolysin-derived peptide


Mass: 1825.995 Da / Num. of mol.: 2
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
#4: 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 / 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
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Sodium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→38.4 Å / Num. obs: 22483 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 8
Reflection shellResolution: 3→3.1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2197 / CC1/2: 0.661

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Processing

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

4p5k


Resolution: 3.04→38.4 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1123 5 %
Rwork0.2173 21347 -
obs0.2194 22470 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.42 Å2 / Biso mean: 82.0719 Å2 / Biso min: 48.64 Å2
Refinement stepCycle: final / Resolution: 3.04→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 56 0 6136
Biso mean--122.33 --
Num. residues----738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026320
X-RAY DIFFRACTIONf_angle_d0.5478610
X-RAY DIFFRACTIONf_dihedral_angle_d15.632270
X-RAY DIFFRACTIONf_chiral_restr0.042916
X-RAY DIFFRACTIONf_plane_restr0.0041128
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.04-3.180.40371380.32232615100
3.18-3.350.33271360.29322594100
3.35-3.560.31881400.25712634100
3.56-3.830.26591370.22242622100
3.83-4.210.26531400.2142655100
4.22-4.820.21091400.17692665100
4.82-6.070.23421420.192705100
6.07-38.40.23331500.2062285799
Refinement TLS params.Method: refined / Origin x: -24.7614 Å / Origin y: -23.275 Å / Origin z: -27.1993 Å
111213212223313233
T0.3402 Å2-0.0122 Å2-0.0264 Å2-0.9107 Å20.0415 Å2--0.612 Å2
L0.1115 °20.7933 °20.272 °2-2.9486 °20.328 °2--0.2635 °2
S0.1862 Å °-0.0259 Å °0.0028 Å °0.1392 Å °-0.293 Å °-0.1257 Å °0.035 Å °0.0072 Å °0.1209 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 181
2X-RAY DIFFRACTION1allB3 - 190
3X-RAY DIFFRACTION1allC-1 - 10
4X-RAY DIFFRACTION1allD1 - 181
5X-RAY DIFFRACTION1allE3 - 190
6X-RAY DIFFRACTION1allF-1 - 10

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