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- PDB-4wsg: Crystal Structure of Soluble WR PIV5 F-GCNt -

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Basic information

Entry
Database: PDB / ID: 4wsg
TitleCrystal Structure of Soluble WR PIV5 F-GCNt
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Viral fusion protein / trimer / parainfluenza virus 5 (PIV5) / paramyxovirus / ectodomain / F protein / stability / fusion / prefusion
Function / homology
Function and homology information


viral budding from plasma membrane / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
Head and neck region of the ectodomain of NDV fusion glycoprotein / Newcastle disease virus like domain / Head and neck region of the ectodomain of NDV fusion glycoprotein / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Classic Zinc Finger / Double Stranded RNA Binding Domain / Immunoglobulin-like / Beta Barrel / Sandwich ...Head and neck region of the ectodomain of NDV fusion glycoprotein / Newcastle disease virus like domain / Head and neck region of the ectodomain of NDV fusion glycoprotein / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Classic Zinc Finger / Double Stranded RNA Binding Domain / Immunoglobulin-like / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesParainfluenza virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsPoor, T.A. / Song, A.S. / Welch, B.D. / Kors, C.A. / Jardetzky, T.S. / Lamb, R.A.
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structure of Soluble WR PIV5 F-GCNt
Authors: Poor, T.A. / Song, A.S. / Welch, B.D. / Kors, C.A. / Jardetzky, T.S. / Lamb, R.A.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy / Structure summary
Category: diffrn_detector / entity ...diffrn_detector / entity / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _entity.pdbx_description ..._diffrn_detector.detector / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6097
Polymers160,7243
Non-polymers8854
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18550 Å2
ΔGint-133 kcal/mol
Surface area62390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.528, 155.523, 157.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Fusion glycoprotein F0


Mass: 53574.691 Da / Num. of mol.: 3 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parainfluenza virus 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9YZA2, UniProt: P04849*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.09 M Carboxylic acids (Na-Formate, NH4-Acetate, Na3-Citrate, NaK-Tartrate (racemic), Na-Oxamate); 0.09 M Tris/Bicine; and 27% wt/vol Glycerol/PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07808 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07808 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 41057 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Χ2: 1.302 / Net I/av σ(I): 14.641 / Net I/σ(I): 5.9 / Num. measured all: 209764
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.114.80.6137211.02990.8
3.11-3.234.90.49138761.07294.3
3.23-3.3850.38840581.18398.7
3.38-3.565.20.32741141.273100
3.56-3.785.30.23141471.347100
3.78-4.075.30.15741431.343100
4.07-4.485.20.10241561.356100
4.48-5.135.20.08841871.591100
5.13-6.455.20.08542331.369100
6.45-354.90.04444221.365100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B9B

2b9b


Resolution: 3→34.853 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 1995 4.87 %
Rwork0.2304 38974 -
obs0.2329 40969 97.46 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.934 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 172.38 Å2 / Biso mean: 83.3827 Å2 / Biso min: 43.98 Å2
Baniso -1Baniso -2Baniso -3
1-61.6557 Å2-0 Å2-0 Å2
2---32.9326 Å20 Å2
3----28.7231 Å2
Refinement stepCycle: final / Resolution: 3→34.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10680 0 56 0 10736
Biso mean--83.51 --
Num. residues----1435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110887
X-RAY DIFFRACTIONf_angle_d1.31714863
X-RAY DIFFRACTIONf_chiral_restr0.0791949
X-RAY DIFFRACTIONf_plane_restr0.0051878
X-RAY DIFFRACTIONf_dihedral_angle_d17.3553931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9812-3.05570.49571110.39172189X-RAY DIFFRACTION77
3.0557-3.13820.42351350.34772598X-RAY DIFFRACTION93
3.1382-3.23050.40641390.33282701X-RAY DIFFRACTION95
3.2305-3.33470.36451400.29852770X-RAY DIFFRACTION99
3.3347-3.45380.32081460.27442848X-RAY DIFFRACTION100
3.4538-3.5920.32621440.25542806X-RAY DIFFRACTION100
3.592-3.75520.29771470.23612842X-RAY DIFFRACTION100
3.7552-3.9530.27931430.21712831X-RAY DIFFRACTION100
3.953-4.20030.24421450.19012840X-RAY DIFFRACTION100
4.2003-4.52390.2561470.16572846X-RAY DIFFRACTION100
4.5239-4.9780.19761450.17162852X-RAY DIFFRACTION100
4.978-5.69560.28481500.2242888X-RAY DIFFRACTION100
5.6956-7.16570.33281500.25382924X-RAY DIFFRACTION100
7.1657-34.8550.2091530.20223039X-RAY DIFFRACTION100

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