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- PDB-4gip: Structure of the cleavage-activated prefusion form of the parainf... -

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Basic information

Entry
Database: PDB / ID: 4gip
TitleStructure of the cleavage-activated prefusion form of the parainfluenza virus 5 (PIV5) fusion protein
Components
  • Fusion glycoprotein F1
  • Fusion glycoprotein F2
KeywordsVIRAL PROTEIN / PIV5 / viral fusion protein / membrane fusion / protease cleavage-activated form / ectodomain / trimer / HN (hemagglutinin-neuraminidase)
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
Helicase, Ruva Protein; domain 3 - #110 / 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 / Helicase, Ruva Protein; domain 3 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix non-globular / Special / Immunoglobulin-like ...Helicase, Ruva Protein; domain 3 - #110 / 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 / Helicase, Ruva Protein; domain 3 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix non-globular / Special / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesSimian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWelch, B.D. / Liu, Y. / Kors, C.A. / Leser, G.P. / Jardetzky, T.S. / Lamb, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein.
Authors: Welch, B.D. / Liu, Y. / Kors, C.A. / Leser, G.P. / Jardetzky, T.S. / Lamb, R.A.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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 F2
D: Fusion glycoprotein F1
B: Fusion glycoprotein F2
E: Fusion glycoprotein F1
C: Fusion glycoprotein F2
F: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,13017
Polymers158,6976
Non-polymers2,43311
Water17,132951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46500 Å2
ΔGint-306 kcal/mol
Surface area56580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.930, 140.520, 84.600
Angle α, β, γ (deg.)90.00, 99.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fusion glycoprotein F2


Mass: 8956.415 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Strain: W3 / Gene: F / Plasmid: pBACgus-11 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P04849
#2: Protein Fusion glycoprotein F1


Mass: 43942.520 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 103-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Strain: W3 / Gene: F / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P04849
#3: 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.: 11
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 951 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAINS (A,D), (B,E), (C,F) WERE FORMED BY TRYPSIN TREATMENT

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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: 4.63 Å3/Da / Density % sol: 73.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.15 M ammonium citrate dibasic pH 5.5, 15% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 122300 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2-2.032.7177.8
2.03-2.072.9180.9
2.07-2.113.2184.2
2.11-2.153.4188.9
2.15-2.23.7192.5
2.2-2.253.9194.2
2.25-2.314.2197.7
2.31-2.374.4199.4
2.37-2.444.7199.9
2.44-2.524.8199.9
2.52-2.614.911000.787
2.61-2.71511000.575
2.71-2.845.111000.466
2.84-2.995.111000.314
2.99-3.175.211000.218
3.17-3.425.211000.154
3.42-3.765.211000.127
3.76-4.315.1199.90.107
4.31-5.435.1199.70.072
5.43-504.9199.20.053

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.54 Å
Translation2.5 Å35.54 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B9B

2b9b


Resolution: 2→35.54 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / Phase error: 32.92 / Stereochemistry target values: ML
Details: DIFFRACTION DATA WERE ANISOTROPIC WITH A HIGH RESOLUTION CUTOFF BETWEEN 2-3A. THEREFORE, DATA WERE PROCESSED TO 2A AND SUBMITTED TO THE UCLA MBI DIFFRACTION ANISOTROPY SERVER FOR ELLIPSOIDAL ...Details: DIFFRACTION DATA WERE ANISOTROPIC WITH A HIGH RESOLUTION CUTOFF BETWEEN 2-3A. THEREFORE, DATA WERE PROCESSED TO 2A AND SUBMITTED TO THE UCLA MBI DIFFRACTION ANISOTROPY SERVER FOR ELLIPSOIDAL TRUNCATION AND ANISOTROPIC SCALING. THIS PROCESS MAKES USE OF THE HIGHEST RESOLUTION DATA AVAILABLE, BUT RESULTS IN APPARENTLY LOW COMPLETENESS. USING CUTOFF CRITERIA OF F/SIGMA GREATER THAN EQUAL TO 3, THE SERVER APPLIED RESOLUTION CUTOFF LIMITS OF 1/3.0, 1/2.0, AND 1/2.2 A-1 ALONG THE THREE PRINCIPLE AXES A*, B*, AND C*, RESPECTIVELY. THE SERVER ALSO APPLIED AN ISOTROPIC B-FACTOR OF -22.75 A2. FOR COMPARISON, DATA PROCESSED TO 2.55A WITH NO ANISOTROPY CORRECTION WERE MORE COMPLETE BUT YIELDED POORER ELECTRON DENSITY MAPS (COMPLETENESS = 99.9% (100%),REDUNDANCY = 5.1 (4.9), RMERGE (LINEAR) = 0.118 (0.765))
RfactorNum. reflection% reflection
Rfree0.243 5825 5 %
Rwork0.22 --
obs0.221 116428 59.8 %
all-122300 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.07 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 45.92 Å2
Baniso -1Baniso -2Baniso -3
1--3.1903 Å20 Å2-1.2057 Å2
2--1.4611 Å2-0 Å2
3---1.7292 Å2
Refinement stepCycle: LAST / Resolution: 2→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10230 0 154 951 11335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110539
X-RAY DIFFRACTIONf_angle_d1.13714372
X-RAY DIFFRACTIONf_dihedral_angle_d15.3643835
X-RAY DIFFRACTIONf_chiral_restr0.0671892
X-RAY DIFFRACTIONf_plane_restr0.0051802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02120.170850.201470X-RAY DIFFRACTION1
2.0212-2.04490.191490.2319202X-RAY DIFFRACTION3
2.0449-2.06990.1798140.2306339X-RAY DIFFRACTION5
2.0699-2.09610.3386250.231458X-RAY DIFFRACTION8
2.0961-2.12360.2517290.2548626X-RAY DIFFRACTION10
2.1236-2.15270.2514510.2484843X-RAY DIFFRACTION14
2.1527-2.18350.2766620.24841082X-RAY DIFFRACTION18
2.1835-2.21610.2481800.24471401X-RAY DIFFRACTION23
2.2161-2.25070.26481000.27531772X-RAY DIFFRACTION29
2.2507-2.28760.31581190.25612242X-RAY DIFFRACTION36
2.2876-2.3270.29541090.25572540X-RAY DIFFRACTION41
2.327-2.36930.29031500.25712917X-RAY DIFFRACTION47
2.3693-2.41490.2741690.27133243X-RAY DIFFRACTION52
2.4149-2.46420.28221600.27563508X-RAY DIFFRACTION57
2.4642-2.51770.30271980.27043819X-RAY DIFFRACTION62
2.5177-2.57630.30182090.2614149X-RAY DIFFRACTION67
2.5763-2.64070.30422300.27344485X-RAY DIFFRACTION72
2.6407-2.71210.28492870.26724738X-RAY DIFFRACTION78
2.7121-2.79180.27832710.27255133X-RAY DIFFRACTION84
2.7918-2.88190.28032710.2715587X-RAY DIFFRACTION90
2.8819-2.98490.33472970.27115985X-RAY DIFFRACTION97
2.9849-3.10430.28233350.26396136X-RAY DIFFRACTION100
3.1043-3.24550.29063500.24226153X-RAY DIFFRACTION100
3.2455-3.41650.26233240.22826155X-RAY DIFFRACTION100
3.4165-3.63030.22073190.20016158X-RAY DIFFRACTION100
3.6303-3.91030.23153410.18626157X-RAY DIFFRACTION99
3.9103-4.30320.21523190.17556129X-RAY DIFFRACTION99
4.3032-4.92450.16713220.16726141X-RAY DIFFRACTION99
4.9245-6.1990.21163380.18976197X-RAY DIFFRACTION100
6.199-35.550.20973320.19826238X-RAY DIFFRACTION99

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