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- PDB-8kb0: Crystal structure of 01JD-AEAIIVAMV -

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Basic information

Entry
Database: PDB / ID: 8kb0
TitleCrystal structure of 01JD-AEAIIVAMV
Components
  • Beta2-microglobulin
  • MHC class I antigen alpha chain
  • 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: 2.48 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
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen alpha chain
B: Beta2-microglobulin
C: peptide of AIV
D: MHC class I antigen alpha chain
E: Beta2-microglobulin
F: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)88,5326
Polymers88,5326
Non-polymers00
Water4,125229
1
A: MHC class I antigen alpha chain
B: Beta2-microglobulin
C: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,2663
Polymers44,2663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-15 kcal/mol
Surface area18860 Å2
MethodPISA
2
D: MHC class I antigen alpha chain
E: Beta2-microglobulin
F: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,2663
Polymers44,2663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-20 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.706, 89.237, 117.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen alpha chain


Mass: 31486.705 Da / Num. of mol.: 2
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 Beta2-microglobulin


Mass: 11863.242 Da / Num. of mol.: 2
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.: 2
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.: 229 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277.15 K / Method: lipidic cubic phase
Details: 0.2M Ammonium acetate 0.1M HEPES pH 7.5 25% w/v PEG 3350

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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: 2.48→71.14 Å / Num. obs: 30537 / % possible obs: 92.7 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.038 / Rrim(I) all: 0.138 / Χ2: 0.96 / Net I/σ(I): 14.6 / Num. measured all: 398097
Reflection shellResolution: 2.48→2.61 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.159 / Num. measured all: 64311 / Num. unique obs: 4712 / CC1/2: 0.888 / Rpim(I) all: 0.324 / Rrim(I) all: 1.204 / Χ2: 0.9 / Net I/σ(I) obs: 2.5

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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: 2.48→19.99 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 1898 6.62 %
Rwork0.2032 --
obs0.208 28668 87.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6162 0 0 229 6391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016313
X-RAY DIFFRACTIONf_angle_d1.0318564
X-RAY DIFFRACTIONf_dihedral_angle_d6.531849
X-RAY DIFFRACTIONf_chiral_restr0.053872
X-RAY DIFFRACTIONf_plane_restr0.0111128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.540.32741340.26251780X-RAY DIFFRACTION84
2.54-2.610.32461260.24111834X-RAY DIFFRACTION85
2.61-2.650.3723830.2491142X-RAY DIFFRACTION88
2.7-2.770.31511000.24781517X-RAY DIFFRACTION87
2.77-2.870.30061490.2451964X-RAY DIFFRACTION92
2.87-2.980.33421480.23512021X-RAY DIFFRACTION93
2.98-3.120.32451480.23142071X-RAY DIFFRACTION96
3.12-3.280.25731450.21712127X-RAY DIFFRACTION97
3.28-3.490.27961460.20872116X-RAY DIFFRACTION98
3.49-3.750.29811400.19691782X-RAY DIFFRACTION82
3.75-4.130.24411060.17421645X-RAY DIFFRACTION75
4.13-4.720.19761470.15322220X-RAY DIFFRACTION100
4.72-5.920.25251590.17582234X-RAY DIFFRACTION100
5.92-19.990.25361670.19342317X-RAY DIFFRACTION100

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