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- PDB-9lud: Crystal structure of 9-mer peptide from H5N1 avian influenza viru... -

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Basic information

Entry
Database: PDB / ID: 9lud
TitleCrystal structure of 9-mer peptide from H5N1 avian influenza virus in complex with B4 DUCK MHC I (UAA*76)
Components
  • Beta-2-microglobulin
  • ILE-ARG-ASN-LEU-HIS-ILE-PRO-GLU-VAL
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / duck MHC UAA*76 T cell recognition
Function / homology
Function and homology information


response to metal ion / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / external side of plasma membrane / extracellular space / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
H5N1 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsGao, F. / Li, Y.L. / Dai, M.M. / Liao, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Efficient Identification of Tembusu Virus CTL Epitopes in Inbred HBW/B4 Ducks Using a Novel MHC Class I-Restricted Epitope Screening Scheme
Authors: Lin, Z. / Zhang, N.Z.
History
DepositionFeb 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: 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: Beta-2-microglobulin
C: ILE-ARG-ASN-LEU-HIS-ILE-PRO-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)44,1393
Polymers44,1393
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.094, 82.094, 111.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein MHC class I antigen


Mass: 31459.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: Anpl-UAA01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6M3RI17
#2: Protein Beta-2-microglobulin


Mass: 11586.955 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(DE3) (bacteria) / References: UniProt: Q14U75
#3: Protein/peptide ILE-ARG-ASN-LEU-HIS-ILE-PRO-GLU-VAL


Mass: 1092.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) H5N1 subtype (virus)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Salt: none Buffer: 0.04 M Citric acid, 0.06 M BIS-TRIS propane / pH 6.4 Polymer: 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.5→44 Å / Num. obs: 14802 / % possible obs: 99.2 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.9
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.166 / Num. unique obs: 1578

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.501→43.839 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.162 / SU B: 9.577 / SU ML: 0.214 / Average fsc free: 0.9609 / Average fsc work: 0.9806 / Cross valid method: FREE R-VALUE / ESU R: 0.794 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2469 734 5.005 %
Rwork0.1764 13932 -
all0.18 --
obs-14666 99.262 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20.001 Å20 Å2
2--0.003 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.501→43.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 0 129 3224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123181
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162843
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.6774316
X-RAY DIFFRACTIONr_angle_other_deg0.4771.596553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.858529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85310513
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.75910172
X-RAY DIFFRACTIONr_chiral_restr0.0620.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
X-RAY DIFFRACTIONr_nbd_refined0.2110.2582
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22679
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21500
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.219
X-RAY DIFFRACTIONr_nbd_other0.1690.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2610.213
X-RAY DIFFRACTIONr_mcbond_it2.5882.8391513
X-RAY DIFFRACTIONr_mcbond_other2.5842.8391513
X-RAY DIFFRACTIONr_mcangle_it4.0235.0891886
X-RAY DIFFRACTIONr_mcangle_other4.0225.0891887
X-RAY DIFFRACTIONr_scbond_it3.3943.2091668
X-RAY DIFFRACTIONr_scbond_other3.3933.2091669
X-RAY DIFFRACTIONr_scangle_it5.2985.692430
X-RAY DIFFRACTIONr_scangle_other5.2975.692431
X-RAY DIFFRACTIONr_lrange_it7.19727.9153479
X-RAY DIFFRACTIONr_lrange_other7.19527.7923466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.501-2.5660.222520.2159910.21611040.9710.97794.47460.188
2.566-2.6360.284510.2179700.2210580.9590.97696.50280.193
2.636-2.7120.325510.2119660.21710240.9370.97599.31640.183
2.712-2.7950.31500.2069380.2119890.9510.97699.89890.177
2.795-2.8860.347480.1989210.2059690.9380.9781000.17
2.886-2.9870.284470.1918820.1969290.9580.9771000.168
2.987-3.0990.269450.1838670.1879120.9580.9791000.164
3.099-3.2250.224440.1888270.1898710.9680.981000.173
3.225-3.3680.245420.1987930.28350.9640.9781000.185
3.368-3.5310.346390.1947580.2017980.9420.9899.87470.183
3.531-3.7210.25390.1757250.1797640.9630.9851000.163
3.721-3.9450.224360.1666980.1697340.9660.9851000.157
3.945-4.2140.206340.1496360.1526700.9740.9881000.142
4.214-4.5490.17310.1345920.1366230.9820.9891000.133
4.549-4.9770.192290.1365550.1395840.9810.991000.137
4.977-5.5560.204270.1385100.1415370.9790.991000.135
5.556-6.3980.268230.1644470.1694700.9590.9851000.159
6.398-7.7950.271200.1843730.1883930.9720.9811000.178
7.795-10.8530.191160.1433020.1463180.9820.9871000.151
10.853-43.8390.238100.2271810.2281910.9560.9721000.232

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