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- PDB-5y0w: The structure of RVFV Gn head domain -

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Basic information

Entry
Database: PDB / ID: 5y0w
TitleThe structure of RVFV Gn head domain
ComponentsNSmGnGc
KeywordsVIRAL PROTEIN / RVFV / Glycoprotein N (Gn) / bunyavirus / phlebovirus
Function / homology
Function and homology information


host cell mitochondrial outer membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, Y. / Gao, F. / Qi, J.X. / Chai, Y. / Gao, G.F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of phlebovirus glycoprotein Gn and identification of a neutralizing antibody epitope
Authors: Wu, Y. / Zhu, Y.H. / Gao, F. / Jiao, Y.J. / Oladejo, B.O. / Chai, Y. / Bi, Y.H. / Lu, S. / Dong, M.Q. / Zhang, C. / Huang, G.M. / Wong, G. / Li, N. / Zhang, Y.F. / Li, Y. / Feng, W.H. / Shi, ...Authors: Wu, Y. / Zhu, Y.H. / Gao, F. / Jiao, Y.J. / Oladejo, B.O. / Chai, Y. / Bi, Y.H. / Lu, S. / Dong, M.Q. / Zhang, C. / Huang, G.M. / Wong, G. / Li, N. / Zhang, Y.F. / Li, Y. / Feng, W.H. / Shi, Y. / Liang, M.F. / Zhang, R.G. / Qi, J.X. / Gao, G.F.
History
DepositionJul 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: NSmGnGc


Theoretical massNumber of molelcules
Total (without water)35,7701
Polymers35,7701
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.571, 73.874, 98.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NSmGnGc / glycoprotein N


Mass: 35769.699 Da / Num. of mol.: 1 / Fragment: UNP residues 154-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: H9BSP3, UniProt: P03518*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M MES, pH 6.5, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13526 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.774 / Num. unique obs: 1286 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.87 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.2483 597 4.97 %
Rwork0.1967 --
obs0.1994 12020 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 0 60 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152498
X-RAY DIFFRACTIONf_angle_d1.7873352
X-RAY DIFFRACTIONf_dihedral_angle_d16.63935
X-RAY DIFFRACTIONf_chiral_restr0.097359
X-RAY DIFFRACTIONf_plane_restr0.01437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4945-2.74550.3694900.26641846X-RAY DIFFRACTION58
2.7455-3.14270.29081610.2483006X-RAY DIFFRACTION95
3.1427-3.95890.26971800.20253209X-RAY DIFFRACTION100
3.9589-40.87560.19161660.15953362X-RAY DIFFRACTION100
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)
10.7496-0.72540.4292.01450.90811.9447-0.0385-0.03790.0207-0.2095-0.09190.0179-0.5817-0.03820.06130.2818-0.0218-0.050.1679-0.01550.1913115.3989228.98688.7591
20.32330.08-0.17760.69990.67062.065-0.01730.0126-0.0085-0.1431-0.0122-0.0534-0.20240.14260.04650.1192-0.0226-0.02050.1763-0.00080.1856121.1178219.94619.4645
31.4394-1.5025-0.4053.0847-0.90771.32-0.0920.1116-0.1842-0.0074-0.00990.2871-0.3361-0.14480.10410.23870.0484-0.05030.2114-0.02020.2047105.0975239.487733.0748
40.19620.2130.09110.9170.93132.9024-0.0011-0.1250.05880.225-0.1462-0.24260.2883-0.1193-0.00280.14670.0459-0.02520.21330.03410.2036123.4516211.121216.0238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 224 )
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 316 )

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