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- PDB-7pdy: A viral peptide from Marek's disease virus bound to chicken MHC-I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pdy | ||||||
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Title | A viral peptide from Marek's disease virus bound to chicken MHC-II molecule | ||||||
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![]() | IMMUNE SYSTEM / MDV / Viral infection / chicken / MHC-II / B21 haplotype | ||||||
Function / homology | ![]() 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 / membrane => GO:0016020 / immune response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() Marek's disease herpesvirus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goryanin, A. / Cook, A.G. / Kaufman, J. / Halabi, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Viral peptide bound to chicken MHC-II molecule Authors: Goryanin, A. / Cook, A.G. / Kaufman, J. / Halabi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 481 KB | Display | ![]() |
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PDB format | ![]() | 396.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kvmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 21970.533 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | 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.) ![]() ![]() ![]() Gene: PP38 / Plasmid: pFastBac1 / Production host: ![]() |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 161 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 4000, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.25 Å2 / Biso mean: 76.821 Å2 / Biso min: 45.97 Å2
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Refinement step | Cycle: final / Resolution: 2.54→206.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.543→2.609 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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