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- PDB-1wp8: crystal structure of Hendra Virus fusion core -

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Basic information

Entry
Database: PDB / ID: 1wp8
Titlecrystal structure of Hendra Virus fusion core
ComponentsFusion glycoprotein F0,Fusion glycoprotein F0
KeywordsVIRAL PROTEIN / Hendra Virus / Fusion Core / heptad repeat
Function / homology
Function and homology information


host cell surface / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
YojJ-like / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsXu, Y. / Liu, Y. / Lou, Z. / Su, N. / Bai, Z. / Gao, G.F. / Rao, Z.
CitationJournal: FEBS J. / Year: 2006
Title: Crystal structures of Nipah and Hendra virus fusion core proteins
Authors: Lou, Z. / Xu, Y. / Xiang, K. / Su, N. / Qin, L. / Li, X. / Gao, G.F. / Bartlam, M. / Rao, Z.
History
DepositionAug 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 7, 2017Group: Database references
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0,Fusion glycoprotein F0
B: Fusion glycoprotein F0,Fusion glycoprotein F0
C: Fusion glycoprotein F0,Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)29,2463
Polymers29,2463
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-53 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.188, 31.897, 53.868
Angle α, β, γ (deg.)86.33, 86.16, 67.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fusion glycoprotein F0,Fusion glycoprotein F0 / fusion


Mass: 9748.781 Da / Num. of mol.: 3 / Fragment: UNP residues 137-178,UNP residues 453-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Genus: Henipavirus / Plasmid: pET 22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O89342
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.7 Å3/Da / Density % sol: 29.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9799, 0.9801, 0.950
DetectorDate: Nov 12, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.98011
30.951
ReflectionResolution: 2.2→35 Å / Num. all: 9875 / Num. obs: 9875
Reflection shellResolution: 2.2→2.25 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→35 Å
RfactorNum. reflection
Rfree0.2739 504
Rwork0.2129 -
obs0.2129 9483
all-10071
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 0 183 1670

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