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- PDB-5tdl: Crystal structure of prefusion-stabilized bovine RSV fusion glyco... -

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Basic information

Entry
Database: PDB / ID: 5tdl
TitleCrystal structure of prefusion-stabilized bovine RSV fusion glycoprotein (single-chain DS2-v1 variant: strain 391-2 sc9 DS-Cav1 Q98C Q361C)
ComponentsBovine prefusion RSV F glycoprotein
KeywordsVIRAL PROTEIN / Bovine RSV F / pre-fusion stabilized / single chain
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / virion component / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Fusion glycoprotein F0
Similarity search - Component
Biological speciesBovine respiratory syncytial virus
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsChen, L. / Zhang, B. / Kwong, P.D.
CitationJournal: NPJ Vaccines / Year: 2017
Title: Protection of calves by a prefusion-stabilized bovine RSV F vaccine.
Authors: Zhang, B. / Chen, L. / Silacci, C. / Thom, M. / Boyington, J.C. / Druz, A. / Joyce, M.G. / Guzman, E. / Kong, W.P. / Lai, Y.T. / Stewart-Jones, G.B.E. / Tsybovsky, Y. / Yang, Y. / Zhou, T. / ...Authors: Zhang, B. / Chen, L. / Silacci, C. / Thom, M. / Boyington, J.C. / Druz, A. / Joyce, M.G. / Guzman, E. / Kong, W.P. / Lai, Y.T. / Stewart-Jones, G.B.E. / Tsybovsky, Y. / Yang, Y. / Zhou, T. / Baxa, U. / Mascola, J.R. / Corti, D. / Lanzavecchia, A. / Taylor, G. / Kwong, P.D.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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_conn / 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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bovine prefusion RSV F glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2242
Polymers59,0021
Non-polymers2211
Water0
1
A: Bovine prefusion RSV F glycoprotein
hetero molecules

A: Bovine prefusion RSV F glycoprotein
hetero molecules

A: Bovine prefusion RSV F glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,6716
Polymers177,0073
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13560 Å2
ΔGint-32 kcal/mol
Surface area56160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.072, 172.072, 172.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Bovine prefusion RSV F glycoprotein / Collar protein / Whisker antigen control protein


Mass: 59002.352 Da / Num. of mol.: 1 / Mutation: Q98C, I144S, S155C, S190F, V207L, S290C, Q361C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine respiratory syncytial virus (strain Copenhagen), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: Copenhagen / Gene: wac / Production host: Homo sapiens (human) / References: UniProt: P22167, UniProt: P10104
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.9 M of potassium and sodium tartrate, 0.16 M of Lithium sulfate, 0.1 M ches

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→40.558 Å / Num. obs: 11445 / % possible obs: 99.48 % / Redundancy: 10.4 % / Net I/σ(I): 9.6
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 3.5→40.558 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.15
RfactorNum. reflection% reflection
Rfree0.272 572 5 %
Rwork0.2564 --
obs0.2572 11445 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 253.38 Å2 / Biso mean: 162.1473 Å2 / Biso min: 90.12 Å2
Refinement stepCycle: final / Resolution: 3.5→40.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 14 0 3498
Biso mean--188.29 --
Num. residues----450

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