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- PDB-8kcv: Crystal structure of UDA01-CAAMDDFQL -

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Basic information

Entry
Database: PDB / ID: 8kcv
TitleCrystal structure of UDA01-CAAMDDFQL
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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / phagocytic vesicle membrane / extracellular region
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 UDA01
Authors: Tang, Z. / Zhang, N.
History
DepositionAug 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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
B: Beta2-microglobulin
C: peptide of AIV
D: MHC class I antigen
E: Beta2-microglobulin
F: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)88,6576
Polymers88,6576
Non-polymers00
Water5,477304
1
A: MHC class I antigen
B: Beta2-microglobulin
C: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,3283
Polymers44,3283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-17 kcal/mol
Surface area18330 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta2-microglobulin
F: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,3283
Polymers44,3283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-15 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.446, 108.524, 125.310
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


Mass: 31452.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: Du6MHC I
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6I7L1
#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: 1013.146 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.: 304 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 277.15 K / Method: liquid diffusion / Details: BIS-TRIS pH7.5 PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→108.52 Å / Num. obs: 41604 / % possible obs: 83.1 % / Redundancy: 4.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.065 / Rrim(I) all: 0.151 / Χ2: 0.99 / Net I/σ(I): 9.3 / Num. measured all: 204163
Reflection shellResolution: 2.39→2.51 Å / % possible obs: 86.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.692 / Num. measured all: 31003 / Num. unique obs: 6216 / CC1/2: 0.808 / Rpim(I) all: 0.327 / Rrim(I) all: 0.769 / Χ2: 0.87 / Net I/σ(I) obs: 2.4

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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: 2.39→19.97 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 1844 4.77 %
Rwork0.2066 --
obs0.2088 38641 76.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 0 304 6506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086396
X-RAY DIFFRACTIONf_angle_d1.048672
X-RAY DIFFRACTIONf_dihedral_angle_d6.741848
X-RAY DIFFRACTIONf_chiral_restr0.056888
X-RAY DIFFRACTIONf_plane_restr0.0091134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.33431320.26762628X-RAY DIFFRACTION72
2.45-2.520.28441350.25252674X-RAY DIFFRACTION73
2.52-2.60.31081300.2592690X-RAY DIFFRACTION74
2.6-2.70.36481430.25872775X-RAY DIFFRACTION76
2.7-2.80.3131350.27112813X-RAY DIFFRACTION77
2.8-2.930.3051400.25412856X-RAY DIFFRACTION78
2.93-3.080.31521480.24292868X-RAY DIFFRACTION79
3.09-3.280.27841450.22312911X-RAY DIFFRACTION80
3.28-3.530.22261510.20112921X-RAY DIFFRACTION80
3.53-3.880.23911450.17852906X-RAY DIFFRACTION79
3.88-4.440.22631450.15842901X-RAY DIFFRACTION78
4.44-5.570.1511440.14462892X-RAY DIFFRACTION77
5.57-19.970.19961510.19082962X-RAY DIFFRACTION76

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