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- PDB-2b9b: Structure of the Parainfluenza Virus 5 F Protein in its Metastabl... -

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Basic information

Entry
Database: PDB / ID: 2b9b
TitleStructure of the Parainfluenza Virus 5 F Protein in its Metastable, Pre-fusion Conformation
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / fusion protein / pre-fusion conformation
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
Head and neck region of the ectodomain of NDV fusion glycoprotein / 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 / Classic Zinc Finger / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Head and neck region of the ectodomain of NDV fusion glycoprotein / 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 / Classic Zinc Finger / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesSimian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / molecular replacement / Resolution: 2.85 Å
AuthorsYin, H.-S. / Wen, X. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S.
CitationJournal: Nature / Year: 2006
Title: Structure of the parainfluenza virus 5 F protein in its metastable, prefusion conformation
Authors: Yin, H.-S. / Wen, X. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)163,30015
Polymers160,6463
Non-polymers2,65412
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20110 Å2
ΔGint-123 kcal/mol
Surface area63870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.206, 259.864, 154.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fusion glycoprotein F0


Mass: 53548.613 Da / Num. of mol.: 3 / Fragment: residues 20-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Genus: Rubulavirus / Gene: F / Plasmid: pMelBac / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04849
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / 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


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.99 Å3/Da / Density % sol: 75.34 %
Crystal growTemperature: 295 K / pH: 8
Details: sodium potassium tartrate, imidazole, pH 8.00, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9956
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9956 Å / Relative weight: 1
ReflectionResolution: 2.85→39.15 Å / Num. obs: 74802 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 98.2 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.1
Reflection shellResolution: 2.85→3 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2 / Rsym value: 0.376 / % possible all: 99.7

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Phasing

Phasing
Method
MIRAS
molecular replacement
Phasing set
ID
1
2
3
4
5
Phasing MIRResolution: 3→45.46 Å / FOM acentric: 0.082 / FOM centric: 0.123 / Reflection acentric: 59264 / Reflection centric: 4417
Phasing MIR der

Native set-ID: 1 / Resolution: 3→45.46 Å

IDR cullis acentricR cullis centricDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_100100592634414
ISO_21.0841.05520.2570.264172461810
ISO_30.6360.604300171121866
ISO_40.6620.65940.3240.296171481882
ISO_50.6770.6850.4850.456171431878
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
8.3645.46ISO_100002460497
5.968.36ISO_100004694522
4.885.96ISO_100006143567
4.234.88ISO_100007349558
3.794.23ISO_100008438583
3.463.79ISO_100009335574
3.213.46ISO_1000010143562
33.21ISO_1000010701551
8.3645.46ISO_21.1031.0480.4250.3822443459
5.968.36ISO_21.0631.0320.3040.2324693509
4.885.96ISO_21.0811.0760.1470.1326141546
4.234.88ISO_21.0891.0660.0690.0633969296
3.794.23ISO_2000000
3.463.79ISO_2000000
3.213.46ISO_2000000
33.21ISO_2000000
8.3645.46ISO_30.5120.517002445482
5.968.36ISO_30.6360.626004694522
4.885.96ISO_30.6730.672006143567
4.234.88ISO_30.6910.689003830295
3.794.23ISO_3000000
3.463.79ISO_3000000
3.213.46ISO_3000000
33.21ISO_3000000
8.3645.46ISO_40.5310.5970.5280.3982460496
5.968.36ISO_40.6790.6540.3930.3184694522
4.885.96ISO_40.6860.6990.2690.2316143567
4.234.88ISO_40.7110.7260.1630.1423851297
3.794.23ISO_4000000
3.463.79ISO_4000000
3.213.46ISO_4000000
33.21ISO_4000000
8.3645.46ISO_50.620.6650.8250.5722457493
5.968.36ISO_50.6950.6820.480.3734694522
4.885.96ISO_50.6950.6950.1780.146143567
4.234.88ISO_50.7130.7320.0630.0443849296
3.794.23ISO_5000000
3.463.79ISO_5000000
3.213.46ISO_5000000
33.21ISO_5000000
Phasing MIR shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
8.36-45.460.690.562461500
5.96-8.360.3780.2984694522
4.88-5.960.1650.1336143567
4.23-4.880.0540.0567349558
3.79-4.23008438583
3.46-3.79009335574
3.21-3.460010143562
3-3.210010701551

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
SHARPphasing
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
DMphasing
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.85→39.15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2925838.78 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2251 3 %RANDOM
Rwork0.222 ---
obs0.222 74777 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1307 Å2 / ksol: 0.325526 e/Å3
Displacement parametersBiso mean: 65.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.32 Å20 Å20 Å2
2--16.7 Å20 Å2
3----23.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.85→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 168 130 10922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 321 2.6 %
Rwork0.326 11969 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM

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