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- PDB-7t6i: Crystal structure of HLA-DP1 in complex with pp65 peptide in reve... -

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Basic information

Entry
Database: PDB / ID: 7t6i
TitleCrystal structure of HLA-DP1 in complex with pp65 peptide in reverse orientation
Components
  • HLA class II histocompatibility antigen DP alpha chain
  • MHC class II antigen
  • pp65 peptide
KeywordsIMMUNE SYSTEM / Antigen presentation
Function / homology
Function and homology information


viral tegument / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane / host cell nucleus
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 ...Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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
GLYCINE / 65 kDa phosphoprotein / HLA class II histocompatibility antigen DP alpha chain / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Human cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLim, J.J. / Reid, H. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Human T cells recognize HLA-DP-bound peptides in two orientations.
Authors: Klobuch, S. / Lim, J.J. / van Balen, P. / Kester, M.G.D. / de Klerk, W. / de Ru, A.H. / Pothast, C.R. / Jedema, I. / Drijfhout, J.W. / Rossjohn, J. / Reid, H.H. / van Veelen, P.A. / ...Authors: Klobuch, S. / Lim, J.J. / van Balen, P. / Kester, M.G.D. / de Klerk, W. / de Ru, A.H. / Pothast, C.R. / Jedema, I. / Drijfhout, J.W. / Rossjohn, J. / Reid, H.H. / van Veelen, P.A. / Falkenburg, J.H.F. / Heemskerk, M.H.M.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 chain
B: MHC class II antigen
C: pp65 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8488
Polymers45,0473
Non-polymers8015
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-18 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.360, 62.364, 72.796
Angle α, β, γ (deg.)90.000, 91.523, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen DP alpha chain / HLA-DPA1 protein / HLA-DPA1*02:01:01:NEW / MHC class II antigen


Mass: 21020.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPA1
Production host: Insect expression vector pBlueBacmsGCA1His (others)
References: UniProt: Q95HB9
#2: Protein MHC class II antigen


Mass: 22173.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPB1, DPB1
Production host: Insect expression vector pBlueBacmsGCB1His (others)
References: UniProt: S6B6U4

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Protein/peptide / Sugars , 2 types, 4 molecules C

#3: Protein/peptide pp65 peptide / pp65 / 65 kDa matrix phosphoprotein / Phosphoprotein UL83 / Tegument protein UL83


Mass: 1853.148 Da / Num. of mol.: 1 / Fragment: residues 142-158 / Source method: obtained synthetically / Source: (synth.) Human cytomegalovirus (strain AD169) / References: UniProt: P06725
#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.: 3 / 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

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Non-polymers , 3 types, 193 molecules

#5: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Sodium Cacodylate pH 6.5 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→45.04 Å / Num. obs: 22454 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.02 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2175 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WEX

3wex


Resolution: 2.3→43.91 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.8108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 1076 4.79 %
Rwork0.1809 21372 -
obs0.183 22448 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 50 191 3273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393165
X-RAY DIFFRACTIONf_angle_d0.56944317
X-RAY DIFFRACTIONf_chiral_restr0.044476
X-RAY DIFFRACTIONf_plane_restr0.0041563
X-RAY DIFFRACTIONf_dihedral_angle_d5.713430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.30831340.23142643X-RAY DIFFRACTION99.14
2.4-2.530.25381440.20662617X-RAY DIFFRACTION99.28
2.53-2.690.23381040.20832682X-RAY DIFFRACTION99.36
2.69-2.90.24951160.20962674X-RAY DIFFRACTION99.54
2.9-3.190.25261280.20782679X-RAY DIFFRACTION99.72
3.19-3.650.24191480.1832668X-RAY DIFFRACTION99.75
3.65-4.60.19691530.14772663X-RAY DIFFRACTION99.89
4.6-43.910.18741490.16132746X-RAY DIFFRACTION99.86

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