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- PDB-6q0s: Crystal Structure of RSV strain B18537 Prefusion-stabilized glyco... -

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Basic information

Entry
Database: PDB / ID: 6q0s
TitleCrystal Structure of RSV strain B18537 Prefusion-stabilized glycoprotein F Variant DS-Cav1
ComponentsFusion glycoprotein F0
KeywordsIMMUNE SYSTEM / Respiratory syncytial virus / structure-based vaccine design
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / 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
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJoyce, M.G. / Bao, A. / Kwong, P.D.
CitationJournal: Pathog Immun / Year: 2019
Title: Crystal Structure and Immunogenicity of the DS-Cav1-Stabilized Fusion Glycoprotein From Respiratory Syncytial Virus Subtype B.
Authors: Joyce, M.G. / Bao, A. / Chen, M. / Georgiev, I.S. / Ou, L. / Bylund, T. / Druz, A. / Kong, W.P. / Peng, D. / Rundlet, E.J. / Van Galen, J.G. / Wang, S. / Yang, Y. / Zhang, B. / Chuang, G.Y. ...Authors: Joyce, M.G. / Bao, A. / Chen, M. / Georgiev, I.S. / Ou, L. / Bylund, T. / Druz, A. / Kong, W.P. / Peng, D. / Rundlet, E.J. / Van Galen, J.G. / Wang, S. / Yang, Y. / Zhang, B. / Chuang, G.Y. / McLellan, J.S. / Graham, B.S. / Mascola, J.R. / Kwong, P.D.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 11, 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
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0386
Polymers61,3071
Non-polymers7315
Water4,738263
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,11318
Polymers183,9213
Non-polymers2,19215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation9_654y+1,z,x-11
Buried area15680 Å2
ΔGint-113 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.874, 167.874, 167.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-938-

HOH

21F-951-

HOH

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Components

#1: Protein Fusion glycoprotein F0


Mass: 61307.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus (subgroup B / strain 18537)
Strain: 18537 / Production host: Homo sapiens (human) / References: UniProt: P13843
#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: 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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.2 M ammonium sulfate, 0.1 M lithium sulfate, 0.1 M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 57616 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.96
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 3616

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMU

4mmu


Resolution: 1.94→34.27 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.212 2921 5.07 %
Rwork0.187 54651 -
obs0.189 57572 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.42 Å2 / Biso mean: 53.63 Å2 / Biso min: 0.13 Å2
Refinement stepCycle: final / Resolution: 1.94→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 70 263 3863
Biso mean--142.47 44.51 -
Num. residues----454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.941-1.97260.3425990.30851888198770
1.9726-2.00660.33591480.28982312246088
2.0066-2.04310.26981420.26742512265495
2.0431-2.08240.25391400.25022585272597
2.0824-2.12490.25161420.22652611275397
2.1249-2.17110.23751370.21292584272197
2.1711-2.22160.22391440.19952600274498
2.2216-2.27710.20931330.1982628276198
2.2771-2.33870.20111490.1892637278699
2.3387-2.40750.20841240.18082643276798
2.4075-2.48510.21531550.18292637279299
2.4851-2.57390.21081360.1742681281799
2.5739-2.6770.22611320.18192657278999
2.677-2.79870.18761470.18612670281798
2.7987-2.94620.19511380.19552667280599
2.9462-3.13070.20281490.19092665281498
3.1307-3.37220.22911380.1812698283699
3.3722-3.71120.18011420.17212721286399
3.7112-4.24740.19691530.16472710286398
4.2474-5.3480.18781500.14972739288997
5.348-34.22670.23161230.21162806292993
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6288-0.6502-0.44674.02762.06542.3028-0.0582-0.035-0.07510.24760.11940.19710.1995-0.02070.07810.20950.0098-0.01050.2170.02720.2482338.7315167.5507194.6862
22.591-0.33112.09131.47071.27044.06860.11691.3538-0.4579-0.76210.0620.12550.65980.6005-0.18070.8819-0.087-0.0620.797-0.15940.5337338.9843150.0629150.8645
31.66640.77550.78280.430.83913.7158-0.00820.4936-0.3698-1.00440.24280.0881-0.14290.4334-0.10240.42740.0583-0.05820.4037-0.08160.376352.3129155.1524176.6996
41.21930.4730.19720.31570.60342.23970.18330.4059-0.473-0.2929-0.10730.22090.9397-0.0762-0.16590.7124-0.0519-0.18720.4679-0.17880.5495335.0156144.2921161.684
52.66480.36950.87621.40990.27434.580.00980.1448-0.3195-0.0209-0.05210.16350.3017-0.26850.07860.3356-0.0216-0.06140.2498-0.0350.3293339.0172153.8064179.9119
61.1218-0.46390.16991.495-0.11210.5382-0.0166-0.15430.15070.1123-0.0015-0.1163-0.03460.0143-0.0080.26210.01230.01860.242-0.00910.2382342.466186.1384199.3889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'F' AND (RESID 26 THROUGH 60 )F0
2X-RAY DIFFRACTION2CHAIN 'F' AND (RESID 61 THROUGH 98 )F0
3X-RAY DIFFRACTION3CHAIN 'F' AND (RESID 99 THROUGH 170 )F0
4X-RAY DIFFRACTION4CHAIN 'F' AND (RESID 171 THROUGH 238 )F0
5X-RAY DIFFRACTION5CHAIN 'F' AND (RESID 239 THROUGH 309 )F0
6X-RAY DIFFRACTION6CHAIN 'F' AND (RESID 310 THROUGH 509 )F0

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