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- PDB-6f8p: Crystal structure of Gn from Rift Valley fever virus -

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Basic information

Entry
Database: PDB / ID: 6f8p
TitleCrystal structure of Gn from Rift Valley fever virus
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / phlebovirus / glycoprotein / bunyavirus / host cell entry
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHalldorsson, S. / Bowden, T.A. / Harlos, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N002091/1 United Kingdom
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Shielding and activation of a viral membrane fusion protein.
Authors: Steinar Halldorsson / Sai Li / Mengqiu Li / Karl Harlos / Thomas A Bowden / Juha T Huiskonen /
Abstract: Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. ...Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. Here, we address the fusion mechanism of Rift Valley fever virus. We determine the crystal structure of the Gn glycoprotein and fit it with the Gc fusion protein into cryo-electron microscopy reconstructions of the virion. Our analysis reveals how the Gn shields the hydrophobic fusion loops of the Gc, preventing premature fusion. Electron cryotomography of virions interacting with membranes under acidic conditions reveals how the fusogenic Gc is activated upon removal of the Gn shield. Repositioning of the Gn allows extension of Gc and insertion of fusion loops in the outer leaflet of the target membrane. These data show early structural transitions that enveloped viruses undergo during host cell entry and indicate that analogous shielding mechanisms are utilized across diverse virus families.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector / _entity_src_gen.plasmid_name
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)34,9591
Polymers34,9591
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.390, 94.180, 97.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoprotein


Mass: 34958.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: B6S219, UniProt: P21401*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% w/v PEG 6000, 0.1 M HEPES pH 7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.97625
SYNCHROTRONDiamond I0321.07146
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 26, 2015
DECTRIS PILATUS 6M2PIXELApr 29, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
21.071461
ReflectionResolution: 1.6→48.995 Å / Num. obs: 46607 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.35
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 9.47 % / Rmerge(I) obs: 1.044 / Num. unique obs: 3369 / CC1/2: 0.818 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXdev_2283refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→48.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67
RfactorNum. reflection% reflection
Rfree0.1989 2308 4.96 %
Rwork0.1651 --
obs0.1667 46533 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.43 Å2 / Biso mean: 35.0946 Å2 / Biso min: 15.18 Å2
Refinement stepCycle: final / Resolution: 1.6→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 0 336 2659
Biso mean---40.54 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172391
X-RAY DIFFRACTIONf_angle_d1.5253226
X-RAY DIFFRACTIONf_chiral_restr0.103344
X-RAY DIFFRACTIONf_plane_restr0.01418
X-RAY DIFFRACTIONf_dihedral_angle_d16.8491482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.63480.31791540.294927062860
1.6348-1.67280.26911520.254226852837
1.6728-1.71470.2381450.234327472892
1.7147-1.7610.2361510.207726912842
1.761-1.81290.26821610.192827192880
1.8129-1.87140.24331610.181727362897
1.8714-1.93830.22111450.172427072852
1.9383-2.01590.18021360.155727412877
2.0159-2.10760.20491560.161727312887
2.1076-2.21870.19741370.161627622899
2.2187-2.35770.21881370.166527792916
2.3577-2.53980.21361150.173227762891
2.5398-2.79530.1751330.163327982931
2.7953-3.19980.18851330.161728182951
3.1998-4.03110.17211530.145728312984
4.0311-49.0180.18581390.151729983137
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)
11.24640.3342-0.94553.09661.9233.0498-0.3034-0.0643-0.22150.48920.02110.19860.82710.20180.15520.35650.04740.09380.1778-0.00140.246710.336384.35323.676
21.5821-0.7959-0.88893.04233.28483.78-0.2453-0.2793-0.16680.80080.2507-0.0190.84380.56530.05280.37950.09870.01750.22730.0390.204513.496193.719935.8462
30.1206-0.1978-0.10571.6392.16393.1220.0064-0.02050.0252-0.2663-0.0610.0744-0.3920.01550.03610.1759-0.0132-0.00060.15020.01260.192211.202693.686615.1
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 154 through 227 )A154 - 227
2X-RAY DIFFRACTION2chain 'A' and (resid 228 through 319 )A228 - 319
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 469 )A320 - 469

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