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- PDB-1ztm: Structure of the Uncleaved Paramyxovirus (hPIV3) Fusion Protein -

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Basic information

Entry
Database: PDB / ID: 1ztm
TitleStructure of the Uncleaved Paramyxovirus (hPIV3) Fusion Protein
ComponentsFusion glycoprotein
KeywordsVIRAL PROTEIN / fusion protein / 6-helix bundle / trimer / post-fusion
Function / homology
Function and homology information


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
Helix Hairpins - #2480 / 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 / YojJ-like / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix Hairpins / Immunoglobulin-like / Beta Barrel ...Helix Hairpins - #2480 / 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 / YojJ-like / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix Hairpins / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman parainfluenza virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsYin, H.S. / Paterson, R.G. / Wen, X. / Lamb, R.A. / Jardetzky, T.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of the uncleaved ectodomain of the paramyxovirus (hPIV3) fusion protein
Authors: Yin, H.S. / Paterson, R.G. / Wen, X. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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 1.5Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein
B: Fusion glycoprotein
C: Fusion glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,1765
Polymers162,7343
Non-polymers4422
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31210 Å2
ΔGint-228 kcal/mol
Surface area52280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.560, 122.170, 195.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion glycoprotein


Mass: 54244.500 Da / Num. of mol.: 3 / Mutation: R106S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parainfluenza virus 3 / Genus: Respirovirus / Strain: WASH-47885-57 / Gene: F / Plasmid: pBacgus-11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P06828
#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.: 2 / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.5 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3000, Tris, NaCl, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B10.9999
SYNCHROTRONAPS 32-ID20.9999
Detector
TypeIDDetector
MARRESEARCH1CCD
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.05→30.02 Å / Num. all: 48676 / Num. obs: 48676 / Redundancy: 10.4 %
Reflection shellResolution: 3.05→3.21 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
DMmodel building
CNS1.1refinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→30.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2204785.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2365 4.9 %RANDOM
Rwork0.217 ---
obs0.217 48675 99.5 %-
all-48675 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9878 Å2 / ksol: 0.273807 e/Å3
Displacement parametersBiso mean: 57 Å2
Baniso -1Baniso -2Baniso -3
1--17.57 Å20 Å20 Å2
2--42.19 Å20 Å2
3----24.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.05→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9403 0 28 1 9432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.321.5
X-RAY DIFFRACTIONc_mcangle_it9.232
X-RAY DIFFRACTIONc_scbond_it8.62
X-RAY DIFFRACTIONc_scangle_it12.232.5
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 395 5 %
Rwork0.335 7577 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4ion.param

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