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- PDB-1g2c: HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION PROTEIN CORE -

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Basic information

Entry
Database: PDB / ID: 1g2c
TitleHUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION PROTEIN CORE
Components(FUSION PROTEIN (F)) x 2
KeywordsVIRAL PROTEIN / membrane fusion / pneumovirus / HRSV
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsZhao, X. / Singh, M. / Malashkevich, V.N. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structural characterization of the human respiratory syncytial virus fusion protein core.
Authors: Zhao, X. / Singh, M. / Malashkevich, V.N. / Kim, P.S.
History
DepositionOct 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 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 PROTEIN (F)
B: FUSION PROTEIN (F)
C: FUSION PROTEIN (F)
D: FUSION PROTEIN (F)
E: FUSION PROTEIN (F)
F: FUSION PROTEIN (F)
G: FUSION PROTEIN (F)
H: FUSION PROTEIN (F)
I: FUSION PROTEIN (F)
J: FUSION PROTEIN (F)
K: FUSION PROTEIN (F)
L: FUSION PROTEIN (F)
M: FUSION PROTEIN (F)
N: FUSION PROTEIN (F)
O: FUSION PROTEIN (F)
P: FUSION PROTEIN (F)
Q: FUSION PROTEIN (F)
R: FUSION PROTEIN (F)
S: FUSION PROTEIN (F)
T: FUSION PROTEIN (F)
U: FUSION PROTEIN (F)
V: FUSION PROTEIN (F)
W: FUSION PROTEIN (F)
X: FUSION PROTEIN (F)


Theoretical massNumber of molelcules
Total (without water)126,32424
Polymers126,32424
Non-polymers00
Water15,997888
1
A: FUSION PROTEIN (F)
B: FUSION PROTEIN (F)
C: FUSION PROTEIN (F)
D: FUSION PROTEIN (F)
E: FUSION PROTEIN (F)
F: FUSION PROTEIN (F)


Theoretical massNumber of molelcules
Total (without water)31,5816
Polymers31,5816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-144 kcal/mol
Surface area11650 Å2
MethodPISA
2
G: FUSION PROTEIN (F)
H: FUSION PROTEIN (F)
I: FUSION PROTEIN (F)
J: FUSION PROTEIN (F)
K: FUSION PROTEIN (F)
L: FUSION PROTEIN (F)


Theoretical massNumber of molelcules
Total (without water)31,5816
Polymers31,5816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-142 kcal/mol
Surface area11740 Å2
MethodPISA
3
M: FUSION PROTEIN (F)
N: FUSION PROTEIN (F)
O: FUSION PROTEIN (F)
P: FUSION PROTEIN (F)
Q: FUSION PROTEIN (F)
R: FUSION PROTEIN (F)


Theoretical massNumber of molelcules
Total (without water)31,5816
Polymers31,5816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-148 kcal/mol
Surface area11280 Å2
MethodPISA
4
S: FUSION PROTEIN (F)
T: FUSION PROTEIN (F)
U: FUSION PROTEIN (F)
V: FUSION PROTEIN (F)
W: FUSION PROTEIN (F)
X: FUSION PROTEIN (F)


Theoretical massNumber of molelcules
Total (without water)31,5816
Polymers31,5816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-150 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.904, 71.539, 76.455
Angle α, β, γ (deg.)81.34, 73.80, 60.72
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsThe biological assembly is a trimer of heterodimer constructed from chain A, B, C,D,E,F

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Components

#1: Protein
FUSION PROTEIN (F) / CELL FUSION GLYCOPROTEIN


Mass: 5653.654 Da / Num. of mol.: 12 / Fragment: RESIDUES 153-209, HRSV F1 HEPTAD REPEAT
Source method: isolated from a genetically manipulated source
Details: FIRST HEPTAD REPEAT / Source: (gene. exp.) Human respiratory syncytial virus / Genus: Pneumovirus / Strain: RSS-2 / Gene: HRSV F / Plasmid: PQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P11209
#2: Protein/peptide
FUSION PROTEIN (F) / CELL FUSION GLYCOPROTEIN


Mass: 4873.347 Da / Num. of mol.: 12 / Fragment: RESIDUES 476-520, HRSV F1 HEPTAD REPEAT
Source method: isolated from a genetically manipulated source
Details: SECOND HEPTAD REPEAT / Source: (gene. exp.) Human respiratory syncytial virus / Genus: Pneumovirus / Strain: RSS-2 / Gene: HRSV F / Plasmid: PQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P11209
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.28 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris-HCl, Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
224-26 %PEG40001reservoir
3200 mMTris-HCl1reservoir
4300 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9816 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9816 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 62470 / Num. obs: 56973 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 1.3 % / Biso Wilson estimate: 40.37 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Num. unique all: 6224 / % possible all: 64.7
Reflection
*PLUS
Num. measured all: 119905
Reflection shell
*PLUS
% possible obs: 64.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: modified polyser SV5

Resolution: 2.3→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1137175.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.286 5085 10.2 %RANDOM
Rwork0.233 ---
obs0.233 50096 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.95 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-4.32 Å2-5.3 Å2
2--2.37 Å24.03 Å2
3----3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 0 888 8942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 824 10.1 %
Rwork0.292 7310 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PA&_1_TOP_1
X-RAY DIFFRACTION2WATER_REP.PARA&_1_TOP_2
X-RAY DIFFRACTION3ION.PARAM&_1_TOP_3
X-RAY DIFFRACTION4&_1_TOP_4
X-RAY DIFFRACTION5&_1_TOP_5
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 54.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.352 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.292

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