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- PDB-8j4g: Crystal structure of 11JD mutant-I62N -

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Basic information

Entry
Database: PDB / ID: 8j4g
TitleCrystal structure of 11JD mutant-I62N
Components
  • Beta-2-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 / membrane
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 / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 11JD mutant-I62N
Authors: Tang, Z. / Zhang, N.
History
DepositionApr 19, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,9296
Polymers88,9296
Non-polymers00
Water3,405189
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,4643
Polymers44,4643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-19 kcal/mol
Surface area18260 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,4643
Polymers44,4643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-20 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.605, 91.866, 117.814
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: 31684.986 Da / Num. of mol.: 2 / Mutation: I62N
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)
References: UniProt: A0A2Z4U0D0
#2: Protein Beta-2-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.: 189 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 277.15 K / Method: liquid diffusion / Details: PEG3350, magnesium chloride hexahydrate

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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: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 33491 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Rrim(I) all: 0.155 / Χ2: 0.914 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.5912.61.04932900.960.990.3041.0930.741100
2.59-2.69130.77432850.980.9950.2210.8060.802100
2.69-2.8213.40.59233190.9880.9970.1660.6150.746100
2.82-2.9613.30.40832820.9920.9980.1150.4240.795100
2.96-3.1512.70.31733140.9950.9990.0920.330.921100
3.15-3.3913.20.20233510.9970.9990.0570.211.065100
3.39-3.7313.20.14633130.9970.9990.0410.1511.12100
3.73-4.27130.11633670.9980.9990.0330.1211.067100
4.27-5.3812.30.09834030.9970.9990.0290.1021.046100
5.38-5011.90.07435670.9980.9990.0220.0770.83399.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→20 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 1398 4.85 %RANDOM
Rwork0.1897 ---
obs0.193 28836 86.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 0 0 189 6379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086358
X-RAY DIFFRACTIONf_angle_d0.9978626
X-RAY DIFFRACTIONf_dihedral_angle_d6.323852
X-RAY DIFFRACTIONf_chiral_restr0.057882
X-RAY DIFFRACTIONf_plane_restr0.0091136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.580.3734660.24321178X-RAY DIFFRACTION38
2.58-2.690.3359970.23351563X-RAY DIFFRACTION50
2.69-2.810.29561080.23572447X-RAY DIFFRACTION77
2.81-2.960.32921630.22763025X-RAY DIFFRACTION97
2.96-3.140.34241770.21963129X-RAY DIFFRACTION100
3.14-3.380.27171510.20533167X-RAY DIFFRACTION100
3.38-3.720.23141690.18243159X-RAY DIFFRACTION100
3.72-4.250.23031450.16543197X-RAY DIFFRACTION100
4.25-5.340.20731720.14873225X-RAY DIFFRACTION100
5.34-200.22231500.18183348X-RAY DIFFRACTION100

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