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- PDB-7pdy: A viral peptide from Marek's disease virus bound to chicken MHC-I... -

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Basic information

Entry
Database: PDB / ID: 7pdy
TitleA viral peptide from Marek's disease virus bound to chicken MHC-II molecule
Components
  • 38 kDa phosphoprotein,MHC class II beta chain
  • MHC class II alpha chain
KeywordsIMMUNE SYSTEM / MDV / Viral infection / chicken / MHC-II / B21 haplotype
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation / MHC class II protein complex / adaptive immune response / immune response / metal ion binding / membrane
Similarity search - Function
Herpesvirus pp38 phosphoprotein / Herpesvirus pp38 phosphoprotein / 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 ...Herpesvirus pp38 phosphoprotein / Herpesvirus pp38 phosphoprotein / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / 38 kDa phosphoprotein / MHC class II alpha chain / MHC class II beta chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
Marek's disease herpesvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsGoryanin, A. / Cook, A.G. / Kaufman, J. / Halabi, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110106/Z/15/Z United Kingdom
CitationJournal: To Be Published
Title: Viral peptide bound to chicken MHC-II molecule
Authors: Goryanin, A. / Cook, A.G. / Kaufman, J. / Halabi, S.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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: MHC class II alpha chain
B: 38 kDa phosphoprotein,MHC class II beta chain
C: MHC class II alpha chain
D: 38 kDa phosphoprotein,MHC class II beta chain
E: MHC class II alpha chain
F: 38 kDa phosphoprotein,MHC class II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,79325
Polymers141,3986
Non-polymers2,39519
Water2,648147
1
A: MHC class II alpha chain
B: 38 kDa phosphoprotein,MHC class II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01911
Polymers47,1332
Non-polymers8879
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-28 kcal/mol
Surface area18770 Å2
MethodPISA
2
C: MHC class II alpha chain
D: 38 kDa phosphoprotein,MHC class II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8448
Polymers47,1332
Non-polymers7126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-28 kcal/mol
Surface area18930 Å2
MethodPISA
3
E: MHC class II alpha chain
F: 38 kDa phosphoprotein,MHC class II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9296
Polymers47,1332
Non-polymers7974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-28 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.538, 238.538, 76.521
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein MHC class II alpha chain / MHC class II antigen alpha / MHC class II antigen alpha chain


Mass: 21970.533 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-LA / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4U5Z6
#2: Protein 38 kDa phosphoprotein,MHC class II beta chain / Phosphoprotein pp38


Mass: 25161.979 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1- ...Details: Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain,Residues 1-33 are a peptide recombinantly linked to the sequence of the MHC-II beta chain
Source: (gene. exp.) Marek's disease herpesvirus (strain MD11/75C/R2), (gene. exp.) Gallus gallus (chicken)
Gene: PP38 / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P68348, UniProt: Q4U5Z9

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Sugars , 2 types, 5 molecules

#3: 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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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 , 4 types, 161 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 4.44 Å3/Da / Density % sol: 72.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 4000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.54→206.58 Å / Num. obs: 81291 / % possible obs: 99.1 % / Redundancy: 20.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.031 / Rrim(I) all: 0.142 / Net I/σ(I): 16.6 / Num. measured all: 1686668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.54-2.6820.84.43231659111550.4050.9884.540.893.8
8.04-206.5819.50.0435326727300.9980.010.04462.799.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6kvm

6kvm


Resolution: 2.54→206.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 23.409 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 4205 5.2 %RANDOM
Rwork0.2157 ---
obs0.2175 77013 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 204.25 Å2 / Biso mean: 76.821 Å2 / Biso min: 45.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 2.54→206.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9224 0 154 147 9525
Biso mean--135.69 69.31 -
Num. residues----1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139637
X-RAY DIFFRACTIONr_bond_other_d0.0060.0178595
X-RAY DIFFRACTIONr_angle_refined_deg1.471.65613122
X-RAY DIFFRACTIONr_angle_other_deg1.4851.58319691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64751154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20122.018560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.069151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2281569
X-RAY DIFFRACTIONr_chiral_restr0.1050.21177
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211085
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022398
LS refinement shellResolution: 2.543→2.609 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 375 -
Rwork0.369 5657 -
all-6032 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9493-0.50040.03330.5356-0.0390.0107-0.0536-0.11940.0733-0.0770.0443-0.01440.0218-0.03830.00930.079-0.0621-0.02070.1902-0.0110.123140.6107-101.8134-9.7971
20.8993-0.1940.19250.2027-0.08950.0556-0.0988-0.24750.2369-0.0030.0242-0.1102-0.0135-0.04180.07460.0544-0.0085-0.0450.2516-0.07660.128248.2602-95.06862.3714
30.41110.04810.71680.05720.17251.42750.0130.12850.06620.0053-0.0365-0.0582-0.00930.08040.02350.03820.0033-0.00470.29380.02710.121610.1389-96.784134.9264
40.3244-0.29590.15370.3405-0.01641.67530.0260.0799-0.03790.0266-0.0078-0.01010.2998-0.1194-0.01820.0963-0.0435-0.03770.2544-0.03870.0433-0.0039-108.761336.3695
51.0246-0.00510.58410.11040.07770.63810.02890.05350.04890.0676-0.00840.04220.04390.0507-0.02040.08630.0488-0.01880.1719-0.02840.1358-19.4075-90.499247.0388
60.927-0.02310.16040.00440.00790.2931-0.02680.12310.28120.005-0.0057-0.0243-0.10520.07830.03250.07150.0011-0.05670.17110.01120.1814-10.2021-78.080943.1313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 204
2X-RAY DIFFRACTION2B-27 - 204
3X-RAY DIFFRACTION3C3 - 204
4X-RAY DIFFRACTION4D-27 - 201
5X-RAY DIFFRACTION5E3 - 201
6X-RAY DIFFRACTION6F-28 - 201

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