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- PDB-8wo9: Duck major histocompatibility complex class-1 02JD-IMFSNKMAR -

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Basic information

Entry
Database: PDB / ID: 8wo9
TitleDuck major histocompatibility complex class-1 02JD-IMFSNKMAR
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • peptide of AIV
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / extracellular region
Similarity search - Function
: / 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
Beta-2-microglobulin
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTang, Z. / Zhang, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32172871 China
CitationJournal: To Be Published
Title: Structure of duck MHC 02JD
Authors: Tang, Z. / Zhang, N.
History
DepositionOct 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,5763
Polymers44,5763
Non-polymers00
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-23 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.920, 46.300, 95.470
Angle α, β, γ (deg.)90.00, 102.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-603-

HOH

31A-633-

HOH

41A-649-

HOH

51A-653-

HOH

61B-207-

HOH

71B-229-

HOH

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Components

#1: Protein MHC class I antigen


Mass: 31481.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein Beta-2-microglobulin


Mass: 11994.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: b2m
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q14U75
#3: Protein/peptide peptide of AIV


Mass: 1099.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 277.15 K / Method: liquid diffusion
Details: 0.2M Magnesium Chloride hexahydrate 0.1M Tris pH8.5 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→19.003 Å / Num. obs: 72067 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 16.4
Reflection shellResolution: 1.41→1.45 Å / Rmerge(I) obs: 1.6 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 2824 4.95 %
Rwork0.1943 --
obs0.1962 57053 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 0 532 3630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073190
X-RAY DIFFRACTIONf_angle_d0.9374321
X-RAY DIFFRACTIONf_dihedral_angle_d6.008425
X-RAY DIFFRACTIONf_chiral_restr0.06442
X-RAY DIFFRACTIONf_plane_restr0.009568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.28021330.25412709X-RAY DIFFRACTION100
1.58-1.610.29161490.24692723X-RAY DIFFRACTION100
1.61-1.640.27181390.24072648X-RAY DIFFRACTION100
1.64-1.670.29641260.22852723X-RAY DIFFRACTION100
1.67-1.710.28011560.22982690X-RAY DIFFRACTION100
1.71-1.750.26651430.22382657X-RAY DIFFRACTION100
1.75-1.790.25781250.22362752X-RAY DIFFRACTION100
1.79-1.840.26851420.2212721X-RAY DIFFRACTION100
1.84-1.890.2591580.22942659X-RAY DIFFRACTION100
1.89-1.950.23231310.21232678X-RAY DIFFRACTION100
1.95-2.020.25741410.21352703X-RAY DIFFRACTION100
2.02-2.10.23451420.20542712X-RAY DIFFRACTION100
2.1-2.20.23731360.19712721X-RAY DIFFRACTION100
2.2-2.310.25021310.22735X-RAY DIFFRACTION100
2.31-2.460.24831390.20912709X-RAY DIFFRACTION100
2.46-2.650.27341610.20722682X-RAY DIFFRACTION100
2.65-2.910.21321420.20892733X-RAY DIFFRACTION100
2.91-3.330.20511240.18372746X-RAY DIFFRACTION100
3.33-4.190.21891540.15942740X-RAY DIFFRACTION100
4.19-190.1841520.16052788X-RAY DIFFRACTION100

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