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- PDB-8kb1: Crystal structure of 11JD -

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Basic information

Entry
Database: PDB / ID: 8kb1
TitleCrystal structure of 11JD
Components
  • Beta2-microglobulin
  • MHC class I antigen
  • peptide of AIV
KeywordsIMMUNE SYSTEM / major histocompatibility complex / Anpl-UAA
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: 2.46 Å
AuthorsTang, Z. / Zhang, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32172871 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: The impact of micropolymorphism in Anpl-UAA on structural stability and peptide presentation.
Authors: Tang, Z. / Wang, S. / Du, L. / Hu, D. / Chen, X. / Zheng, H. / Ding, H. / Chen, S. / Zhang, L. / Zhang, N.
History
DepositionAug 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 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: Beta2-microglobulin
C: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,4633
Polymers44,4633
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-17 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.593, 87.593, 119.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

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Components

#1: Protein MHC class I antigen


Mass: 31684.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: Anpl-UAA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein Beta2-microglobulin


Mass: 11863.242 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: 916.135 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.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 277.15 K / Method: liquid diffusion / Details: 0.1M HEPES pH 7.5 2.0M Ammonium sulfate

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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: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→70.55 Å / Num. obs: 16047 / % possible obs: 91.2 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.035 / Rrim(I) all: 0.135 / Χ2: 0.96 / Net I/σ(I): 16.4 / Num. measured all: 230035
Reflection shellResolution: 2.46→2.59 Å / % possible obs: 100 % / Redundancy: 15.2 % / Rmerge(I) obs: 1.111 / Num. measured all: 38101 / Num. unique obs: 2514 / CC1/2: 0.905 / Rpim(I) all: 0.293 / Rrim(I) all: 1.15 / Χ2: 0.85 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→41.1 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2901 1510 9.96 %
Rwork0.2081 --
obs0.2161 15165 86.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 0 118 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083199
X-RAY DIFFRACTIONf_angle_d1.024340
X-RAY DIFFRACTIONf_dihedral_angle_d6.869428
X-RAY DIFFRACTIONf_chiral_restr0.057444
X-RAY DIFFRACTIONf_plane_restr0.01571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.540.37511290.2661185X-RAY DIFFRACTION84
2.54-2.610.35661020.2735936X-RAY DIFFRACTION85
2.7-2.730.3561370.254311X-RAY DIFFRACTION89
2.73-2.860.33861430.25351278X-RAY DIFFRACTION91
2.86-3.010.40741480.25831331X-RAY DIFFRACTION94
3.01-3.190.30191510.24221362X-RAY DIFFRACTION97
3.2-3.440.32021530.2281396X-RAY DIFFRACTION97
3.44-3.790.28771550.20431404X-RAY DIFFRACTION98
3.79-4.330.25171580.17581432X-RAY DIFFRACTION99
4.34-5.460.22291620.15371465X-RAY DIFFRACTION100
5.46-41.10.24841720.18441555X-RAY DIFFRACTION100

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