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- PDB-8y74: Crystal structure of 9-mer peptide from H9N2 avian influenza viru... -

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Basic information

Entry
Database: PDB / ID: 8y74
TitleCrystal structure of 9-mer peptide from H9N2 avian influenza virus in complex with BF2*0201
Components
  • Beta-2-microglobulin
  • MHC class I alpha chain 2
  • Polymerase basic protein 2
KeywordsIMMUNE SYSTEM / chicken MHC / T cell recognition
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / virion component / cellular response to nicotine / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular region / cytosol
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / 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
Polymerase basic protein 2 / MHC class I alpha chain 2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJia, Y.S. / Ma, M.L. / Liao, M. / Dai, M.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Revealing novel and conservative T-cell epitopes with MHC B2 restriction on H9N2 avian influenza virus (AIV).
Authors: Jia, Y. / Wu, Q. / Li, Y. / Ma, M. / Song, W. / Chen, R. / Yao, Y. / Nair, V. / Zhang, N. / Liao, M. / Dai, M.
History
DepositionFeb 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I alpha chain 2
B: Beta-2-microglobulin
C: Polymerase basic protein 2
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)87,0136
Polymers87,0136
Non-polymers00
Water4,522251
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)125.782, 76.553, 87.143
Angle α, β, γ (deg.)90.000, 92.449, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I alpha chain 2 / MHC class I antigen / MHC class I glycoprotein / MHC class I molecule


Mass: 31095.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: An extra methionine at the N-terminal of both the A and D chains is encoded by the starting codon ATG.
Source: (gene. exp.) Gallus gallus (chicken) / Gene: BF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O46789
#2: Protein Beta-2-microglobulin


Mass: 11193.601 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21611
#3: Protein/peptide Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 1217.395 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/chicken/Bangladesh/19495/2013(H9N2))
References: UniProt: A0A023PU38
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 7.0, 20% w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.9→43.532 Å / Num. obs: 65173 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4776 / CC1/2: 0.438 / % possible all: 100

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
PHASERphasing
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.532 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.214 / SU B: 9.324 / SU ML: 0.12 / Average fsc free: 0.9581 / Average fsc work: 0.9694 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2402 3321 5.097 %
Rwork0.2039 61831 -
all0.206 --
obs-65152 99.951 %
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: 39.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.321 Å2
2--0.233 Å20 Å2
3---0.293 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6091 0 0 251 6342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165608
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.8268538
X-RAY DIFFRACTIONr_angle_other_deg0.5921.77412907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.879548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48510972
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4810321
X-RAY DIFFRACTIONr_chiral_restr0.0860.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021560
X-RAY DIFFRACTIONr_nbd_refined0.2080.21011
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24954
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22922
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.210
X-RAY DIFFRACTIONr_nbd_other0.110.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.227
X-RAY DIFFRACTIONr_mcbond_it1.5881.7843007
X-RAY DIFFRACTIONr_mcbond_other1.5861.7853007
X-RAY DIFFRACTIONr_mcangle_it2.3843.1933743
X-RAY DIFFRACTIONr_mcangle_other2.3833.1933744
X-RAY DIFFRACTIONr_scbond_it2.3942.0823271
X-RAY DIFFRACTIONr_scbond_other2.3942.0823272
X-RAY DIFFRACTIONr_scangle_it3.6873.6874795
X-RAY DIFFRACTIONr_scangle_other3.6873.6874796
X-RAY DIFFRACTIONr_lrange_it4.91117.8556762
X-RAY DIFFRACTIONr_lrange_other4.86917.816730
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
1.9-1.9490.312490.28445160.28647670.9250.93599.9580.261
1.949-2.0030.2832220.24244830.24447070.950.96499.95750.208
2.003-2.0610.2552240.22642700.22744980.9620.96899.91110.196
2.061-2.1240.2631960.22342300.22544270.960.96999.97740.194
2.124-2.1930.2922180.23240590.23642800.9470.96799.92990.202
2.193-2.270.2442170.22339010.22441270.9610.95999.78190.202
2.27-2.3550.31930.23938030.24239980.9520.96899.950.209
2.355-2.4510.2712160.21936420.22238590.9580.97499.97410.195
2.451-2.560.2512210.21534810.21737020.9610.9741000.198
2.56-2.6840.3091700.22233400.22635100.9470.9721000.211
2.684-2.8290.2771940.2232210.22334150.9520.9711000.217
2.829-30.2481560.2130070.21231630.9610.9741000.214
3-3.2060.2291270.21328800.21330070.9690.9741000.225
3.206-3.4610.2231630.21126100.21227730.970.9791000.223
3.461-3.7890.2261380.20224410.20325790.9740.981000.223
3.789-4.2330.2311180.1722070.17323250.9730.9851000.202
4.233-4.880.192920.14120070.14321000.9810.98999.95240.182
4.88-5.9580.212740.17716690.17817430.980.9861000.215
5.958-8.3470.241810.20313100.20513910.9710.9811000.252
8.347-43.5320.141520.1957530.1918050.9870.9771000.275
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41750.66221.28510.92650.60012.9681-0.00660.12130.0073-0.0710.00710.12040.2094-0.1635-0.00050.06520.00210.01270.0971-0.00040.0663-11.09655.25959.7474
21.83611.26880.38512.70941.41584.52570.0214-0.0854-0.07760.0581-0.12650.21930.4312-0.72730.10510.0711-0.0484-0.00650.1505-0.00390.0462-12.98445.388228.5479
34.16344.70410.078512.5542-0.78552.1777-0.01830.19140.1563-0.34130.05920.55740.2097-0.328-0.04090.1474-0.0032-0.03120.2757-0.02730.1842-25.75650.1026-2.8471
42.1153-0.76410.58542.61790.36343.5377-0.1521-0.06310.12120.0395-0.0391-0.1894-0.3878-0.18480.19120.04970.0229-0.05070.012-0.02560.2289-16.8026-31.444240.2759
52.5541-0.06351.36563.94441.50853.4650.05050.05760.1389-0.2554-0.04810.0385-0.1723-0.2385-0.00250.09030.043-0.00730.11330.02850.1254-27.8164-32.28624.9572
61.3702-3.9902-0.73512.04442.46860.6817-0.2796-0.17930.09480.67520.2013-0.0726-0.0532-0.1390.07830.37960.12780.0310.3338-0.07580.2954-23.698-25.655758.5285
70.1720.2231-0.04050.3458-0.06760.0183-0.03090.0476-0.0476-0.05290.04850.02970.0214-0.0331-0.01760.16770.0288-0.01820.2115-0.01170.164-11.5715-6.366424.1307
80000000000000000.158000.15800.158000
90000000000000000.158000.15800.158000
100000000000000000.158000.15800.158000
110000000000000000.158000.15800.158000
120000000000000000.158000.15800.158000
130000000000000000.158000.15800.158000
140000000000000000.158000.15800.158000
150000000000000000.158000.15800.158000
160000000000000000.158000.15800.158000
170000000000000000.158000.15800.158000
180000000000000000.158000.15800.158000
190000000000000000.158000.15800.158000
200000000000000000.158000.15800.158000
210000000000000000.158000.15800.158000
220000000000000000.158000.15800.158000
230000000000000000.158000.15800.158000
240000000000000000.158000.15800.158000
250000000000000000.158000.15800.158000
260000000000000000.158000.15800.158000
270000000000000000.158000.15800.158000
280000000000000000.158000.15800.158000
290000000000000000.158000.15800.158000
300000000000000000.158000.15800.158000
310000000000000000.158000.15800.158000
320000000000000000.158000.15800.158000
330000000000000000.158000.15800.158000
340000000000000000.158000.15800.158000
350000000000000000.158000.15800.158000
360000000000000000.158000.15800.158000
370000000000000000.158000.15800.158000
380000000000000000.158000.15800.158000
390000000000000000.158000.15800.158000
400000000000000000.158000.15800.158000
410000000000000000.158000.15800.158000
420000000000000000.158000.15800.158000
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 271
2X-RAY DIFFRACTION8ALLA0 - 271
3X-RAY DIFFRACTION15ALLA0 - 271
4X-RAY DIFFRACTION22ALLA0 - 271
5X-RAY DIFFRACTION29ALLA0 - 271
6X-RAY DIFFRACTION36ALLA0 - 271

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