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- PDB-8jqt: Crystal structure of U03-GPAKGIEYD -

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Basic information

Entry
Database: PDB / ID: 8jqt
TitleCrystal structure of U03-GPAKGIEYD
Components
  • Beta-2-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 / 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 alpha chain
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 U03
Authors: Tang, Z. / Zhang, N.
History
DepositionJun 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: Beta-2-microglobulin
C: peptide of AIV


Theoretical massNumber of molelcules
Total (without water)44,6783
Polymers44,6783
Non-polymers00
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-17 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.282, 126.282, 65.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein MHC class I antigen alpha chain


Mass: 31864.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: Anpl-U, Anpl-UAA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6JWQ7
#2: Protein Beta-2-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: 950.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 277.15 K / Method: liquid diffusion / Details: BIS-TRIS pH6.5 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: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 35107 / % possible obs: 99.9 % / Redundancy: 11.6 % / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.072 / Rrim(I) all: 0.243 / Χ2: 0.869 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.037.60.82117500.7110.9120.310.880.50498.8
2.03-2.078.80.7917420.7510.9260.2780.8390.5599.9
2.07-2.119.50.7817440.7990.9420.2630.8240.56199.9
2.11-2.1510.40.72517360.7830.9370.2360.7630.615100
2.15-2.211.90.71917120.7990.9420.2190.7520.637100
2.2-2.2512.30.71217930.8580.9610.2130.7440.806100
2.25-2.3112.40.68717320.8790.9670.2060.7180.767100
2.31-2.3712.30.55817460.9030.9740.1680.5830.799100
2.37-2.4411.90.52217400.9020.9740.160.5460.865100
2.44-2.5212.70.46817630.9340.9830.140.4890.928100
2.52-2.6112.10.42517330.9080.9750.1310.4451.009100
2.61-2.7112.80.38917820.9420.9850.1160.4071.043100
2.71-2.8412.80.35717210.9540.9880.1070.3731.107100
2.84-2.9912.60.30917690.960.990.0940.3231.133100
2.99-3.1711.90.26817620.9710.9930.0840.2811.17499.9
3.17-3.42120.23717620.970.9920.0750.2491.118100
3.42-3.7612.10.20617440.9750.9940.0650.2161.017100
3.76-4.311.90.18417730.9850.9960.0580.1930.904100
4.3-5.3911.50.16517790.9870.9970.0520.1730.806100
5.39-2012.40.15318240.9910.9980.0470.160.649100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→19.78 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1389 4.59 %
Rwork0.1911 --
obs0.1923 30279 86.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 0 360 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083199
X-RAY DIFFRACTIONf_angle_d1.0024343
X-RAY DIFFRACTIONf_dihedral_angle_d6.405426
X-RAY DIFFRACTIONf_chiral_restr0.059438
X-RAY DIFFRACTIONf_plane_restr0.009570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.060.3559470.2704975X-RAY DIFFRACTION29
2.06-2.150.27451060.22241905X-RAY DIFFRACTION58
2.15-2.240.23931340.23882733X-RAY DIFFRACTION81
2.24-2.360.251600.21283201X-RAY DIFFRACTION97
2.36-2.510.25991410.21393335X-RAY DIFFRACTION99
2.51-2.70.21821380.20683331X-RAY DIFFRACTION99
2.7-2.970.22781840.20683301X-RAY DIFFRACTION99
2.97-3.40.2581240.18533378X-RAY DIFFRACTION99
3.4-4.280.1841750.16763331X-RAY DIFFRACTION99
4.28-19.780.16821800.16113400X-RAY DIFFRACTION99

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