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- PDB-4hjc: Crystal structure of glycoprotein C from Rift Valley Fever Virus ... -

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Basic information

Entry
Database: PDB / ID: 4hjc
TitleCrystal structure of glycoprotein C from Rift Valley Fever Virus (non-glycosylated)
ComponentsENVELOPE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / virus entry / class II fusion protein / membrane fusion / viral membrane
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 / fusion of virus membrane with host endosome membrane / symbiont entry into 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 / molecular replacement / Resolution: 4.15 Å
AuthorsDessau, M. / Modis, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of glycoprotein C from Rift Valley fever virus.
Authors: Dessau, M. / Modis, Y.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 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: ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)46,5861
Polymers46,5861
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.347, 114.347, 170.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein ENVELOPE GLYCOPROTEIN / GP / M polyprotein / Non-structural protein NSm / Glycoprotein G1 / Glycoprotein G2


Mass: 46586.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift Valley fever virus / Plasmid: pAc-gp67 / Production host: unidentified baculovirus / References: UniProt: A2T075, UniProt: P03518*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% PEG 5000 MME, 0.1 M MES, O.1 M Ammonium sulfate, 5% glycerol, 1.8 mM UDM, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 4.15→40 Å / Num. all: 5449 / Num. obs: 5438 / % possible obs: 99.8 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 1.4 / Redundancy: 12.6 % / Rmerge(I) obs: 0.075 / Χ2: 0.714 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
4.15-4.2213.52630.4611100
4.22-4.313.12640.4641100
4.3-4.3813.12600.47811000.782
4.38-4.4712.82590.498199.60.711
4.47-4.5712.22640.48111000.483
4.57-4.6713.12550.50911000.462
4.67-4.7913.12700.48211000.33
4.79-4.9213.42600.51711000.318
4.92-5.0612.72660.52211000.299
5.06-5.23122710.52611000.263
5.23-5.4113.62650.60311000.216
5.41-5.6313.32640.58511000.195
5.63-5.8812.82740.58811000.195
5.88-6.1911.92710.65311000.161
6.19-6.58132720.69811000.141
6.58-7.0912.62840.831199.60.101
7.09-7.79122680.92111000.078
7.79-8.9112.52921.201199.70.06
8.91-11.1911.42901.69711000.05
11.19-4010.33261.615198.20.037

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.15→19.988 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6472 / SU ML: 0.55 / σ(F): 1.39 / Phase error: 38.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3112 245 4.6 %
Rwork0.2593 --
obs0.2617 5331 99.85 %
all-5337 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 465.24 Å2 / Biso mean: 173.1681 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 4.15→19.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 5 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043316
X-RAY DIFFRACTIONf_angle_d0.7984463
X-RAY DIFFRACTIONf_chiral_restr0.05503
X-RAY DIFFRACTIONf_plane_restr0.003582
X-RAY DIFFRACTIONf_dihedral_angle_d12.5111191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
4.15-5.21320.36021280.274924672595
5.2132-19.98830.2941170.254426192736
Refinement TLS params.Method: refined / Origin x: 155.7479 Å / Origin y: 150.1085 Å / Origin z: 33.3301 Å
111213212223313233
T0.6542 Å2-0.2953 Å2-0.0097 Å2-0.8659 Å2-0.0539 Å2--0.8004 Å2
L1.516 °2-0.466 °20.7137 °2-0.8961 °2-0.4693 °2--4.5187 °2
S-0.1467 Å °-0.1397 Å °0.0316 Å °-0.2458 Å °-0.1717 Å °-0.1775 Å °0.0323 Å °0.382 Å °0.1855 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA691 - 1118
2X-RAY DIFFRACTION1ALLA1 - 1205

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