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- PDB-2wrd: structure of H2 japan hemagglutinin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2wrd
Titlestructure of H2 japan hemagglutinin
ComponentsHEMAGGLUTININ
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN / LIPOPROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsLiu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: Structures of Receptor Complexes Formed by Hemagglutinins from the Asian Influenza Pandemic of 1957.
Authors: Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
History
DepositionSep 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ
B: HEMAGGLUTININ
C: HEMAGGLUTININ


Theoretical massNumber of molelcules
Total (without water)171,3133
Polymers171,3133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint-38.26 kcal/mol
Surface area57830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.149, 118.365, 221.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 8:323 )
211CHAIN B AND (RESSEQ 5:323 )
311CHAIN C AND (RESSEQ 8:323 )
112CHAIN A AND (RESSEQ 330:354 OR RESSEQ 365:492 )
212CHAIN B AND (RESSEQ 330:492 )
312CHAIN C AND (RESSEQ 330:492 )

NCS ensembles :
ID
1
2

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Components

#1: Protein HEMAGGLUTININ


Mass: 57104.355 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-562 / Source method: isolated from a natural source
Source: (natural) INFLUENZA A VIRUS (A/JAPAN/305+/1957(H2N2))
References: UniProt: Q67085, UniProt: Q0A2X3*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 36750 / % possible obs: 86.4 % / Observed criterion σ(I): 2.1 / Redundancy: 4.5 % / Biso Wilson estimate: 69.52 Å2 / Rmerge(I) obs: 0.12

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3→19.888 Å / SU ML: 0.71 / σ(F): 1.34 / Phase error: 34.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3333 1857 5.1 %
Rwork0.2769 --
obs0.2798 36750 89.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.398 Å2 / ksol: 0.274 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.885 Å20 Å20 Å2
2--0.3031 Å20 Å2
3---4.5819 Å2
Refinement stepCycle: LAST / Resolution: 3→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11367 0 0 0 11367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111642
X-RAY DIFFRACTIONf_angle_d1.30415721
X-RAY DIFFRACTIONf_dihedral_angle_d18.174229
X-RAY DIFFRACTIONf_chiral_restr0.081688
X-RAY DIFFRACTIONf_plane_restr0.0052037
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2471X-RAY DIFFRACTIONPOSITIONAL
12B2471X-RAY DIFFRACTIONPOSITIONAL0.064
13C2471X-RAY DIFFRACTIONPOSITIONAL0.058
21A1227X-RAY DIFFRACTIONPOSITIONAL
22B1227X-RAY DIFFRACTIONPOSITIONAL0.068
23C1223X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.08090.43461340.36092445X-RAY DIFFRACTION84
3.0809-3.17120.36711220.34982498X-RAY DIFFRACTION84
3.1712-3.27320.39921140.32492488X-RAY DIFFRACTION84
3.2732-3.38960.3731370.32592437X-RAY DIFFRACTION83
3.3896-3.52460.42291140.32722450X-RAY DIFFRACTION83
3.5246-3.68410.34331350.31842433X-RAY DIFFRACTION83
3.6841-3.87690.341430.29682393X-RAY DIFFRACTION81
3.8769-4.11780.31391480.24992607X-RAY DIFFRACTION88
4.1178-4.43250.28091530.23642976X-RAY DIFFRACTION100
4.4325-4.87260.27221630.22842971X-RAY DIFFRACTION100
4.8726-5.56420.3131670.2233007X-RAY DIFFRACTION100
5.5642-6.960.30731490.25013070X-RAY DIFFRACTION100
6.96-19.88830.28511780.23923118X-RAY DIFFRACTION99

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