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- PDB-1svf: PARAMYXOVIRUS SV5 FUSION PROTEIN CORE -

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Basic information

Entry
Database: PDB / ID: 1svf
TitlePARAMYXOVIRUS SV5 FUSION PROTEIN CORE
Components(PROTEIN (FUSION GLYCOPROTEIN)) x 2
KeywordsVIRAL PROTEIN / PARAMYXOVIRUS / FUSION / SV5 / COILED-COIL
Function / homology
Function and homology information


viral budding from plasma membrane / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesSimian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsBaker, K.A. / Dutch, R.E. / Lamb, R.A. / Jardetzky, T.S.
CitationJournal: Mol.Cell / Year: 1999
Title: Structural basis for paramyxovirus-mediated membrane fusion.
Authors: Baker, K.A. / Dutch, R.E. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionFeb 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FUSION GLYCOPROTEIN)
B: PROTEIN (FUSION GLYCOPROTEIN)
C: PROTEIN (FUSION GLYCOPROTEIN)
D: PROTEIN (FUSION GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1458
Polymers21,0034
Non-polymers1424
Water5,459303
1
A: PROTEIN (FUSION GLYCOPROTEIN)
B: PROTEIN (FUSION GLYCOPROTEIN)
hetero molecules

A: PROTEIN (FUSION GLYCOPROTEIN)
B: PROTEIN (FUSION GLYCOPROTEIN)
hetero molecules

A: PROTEIN (FUSION GLYCOPROTEIN)
B: PROTEIN (FUSION GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,71812
Polymers31,5056
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14850 Å2
ΔGint-149 kcal/mol
Surface area14040 Å2
MethodPISA
2
C: PROTEIN (FUSION GLYCOPROTEIN)
D: PROTEIN (FUSION GLYCOPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5734
Polymers10,5022
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-146 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.600, 41.600, 95.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21A-103-

CL

31C-100-

CL

41C-102-

CL

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.44279, -1.514, 0.7045)

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Components

#1: Protein PROTEIN (FUSION GLYCOPROTEIN)


Mass: 6432.208 Da / Num. of mol.: 2 / Fragment: POST FUSION CORE (RESIDUE 122-185) / Mutation: C185Y
Source method: isolated from a genetically manipulated source
Details: 4 PUTATIVE CHLORIDE IONS INCLUDED / Source: (gene. exp.) Simian virus 5 (strain W3) / Genus: Rubulavirus / Species: Simian virus 5 / Strain: W3 / Description: CLEAVED GST FUSION; / Gene: FUSION PROTEIN / Plasmid: PGEX-4T-1-N1, PGEX-4T-1-N1 / Gene (production host): N1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: P04849
#2: Protein/peptide PROTEIN (FUSION GLYCOPROTEIN)


Mass: 4069.528 Da / Num. of mol.: 2 / Fragment: POST FUSION CORE (RESIDUE 440-477)
Source method: isolated from a genetically manipulated source
Details: 4 PUTATIVE CHLORIDE IONS INCLUDED / Source: (gene. exp.) Simian virus 5 (strain W3) / Genus: Rubulavirus / Species: Simian virus 5 / Strain: W3 / Description: CLEAVED GST FUSION / Gene: FUSION PROTEIN / Plasmid: PGEX-4T-1-N1, PGEX-4T-1-N1 / Gene (production host): N1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: P04849
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.27 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5
Details: 7-9% POLYETHYLENE GLYCOL 0.5-0.6M LITHIUM SULFATE, pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-HCl1drop
37-9 %PEG80001reservoir
40.5-0.6 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.993
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 1998 / Details: PINHOLE
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 35812 / % possible obs: 98.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 6.3 / Net I/σ(I): 15.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2 / Rsym value: 27.4 / % possible all: 95.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 81223
Reflection shell
*PLUS
% possible obs: 95.8 % / Num. unique obs: 3498 / Num. measured obs: 6738

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Processing

Software
NameVersionClassification
RSPSmodel building
SHARPphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RSPSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→40 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2814 7.9 %SPHERES
Rwork0.181 ---
obs-35812 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.97 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å21.67 Å20 Å2
2--2.59 Å20 Å2
3----5.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 4 303 1737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 420 7.1 %
Rwork0.235 5470 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.252 / % reflection Rfree: 7.1 % / Rfactor Rwork: 0.235

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