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- PDB-6eaf: CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLY... -

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Basic information

Entry
Database: PDB / ID: 6eaf
TitleCRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT G143S STABILIZED IN THE PREFUSION STATE
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / CLASS I VIRAL FUSION PROTEIN / FUSION / RESPIRATORY SYNCYTIAL VIRUS / PREFUSION / FUSION INHIBITOR
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 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBattles, M.B. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI007519-18 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: To be published
Title: Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance
Authors: Battles, M.B. / McLellan, J.S.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)193,03529
Polymers189,7453
Non-polymers3,29026
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-242 kcal/mol
Surface area49420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.249, 167.249, 173.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 26 through 207 or resid 217 through 506))
21(chain B and (resid 26 through 64 or resid 73 through 101 or resid 137 through 506))
31(chain C and (resid 26 through 64 or resid 73 through 207 or resid 217 through 506))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEU(chain A and (resid 26 through 207 or resid 217 through 506))AA26 - 20726 - 207
12ILEILEILEILE(chain A and (resid 26 through 207 or resid 217 through 506))AA217 - 506217 - 506
21GLNGLNILEILE(chain B and (resid 26 through 64 or resid 73 through 101 or resid 137 through 506))BB26 - 6426 - 64
22ASPASPPROPRO(chain B and (resid 26 through 64 or resid 73 through 101 or resid 137 through 506))BB73 - 10173 - 101
23PHEPHEILEILE(chain B and (resid 26 through 64 or resid 73 through 101 or resid 137 through 506))BB137 - 506137 - 506
31GLNGLNILEILE(chain C and (resid 26 through 64 or resid 73 through 207 or resid 217 through 506))CC26 - 6426 - 64
32ASPASPLEULEU(chain C and (resid 26 through 64 or resid 73 through 207 or resid 217 through 506))CC73 - 20773 - 207
33ILEILEILEILE(chain C and (resid 26 through 64 or resid 73 through 207 or resid 217 through 506))CC217 - 506217 - 506

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63248.367 Da / Num. of mol.: 3 / Fragment: RSV F ectodomain / Mutation: S155C, S290C, S190F, V207L, G143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: P(ALPHA)H / Production host: Homo sapiens (human) / Strain (production host): HEK293 FREESTYLE / References: UniProt: W8RJF9, UniProt: P03420*PLUS
#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.: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.19 Å3/Da / Density % sol: 61.49 % / Mosaicity: 0.27 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.60M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→46.88 Å / Num. obs: 49667 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 67.85 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.079 / Rrim(I) all: 0.21 / Net I/σ(I): 7.2 / Num. measured all: 335941 / Scaling rejects: 915
Reflection shellResolution: 3→3.1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.265 / Num. unique obs: 4510 / CC1/2: 0.581 / Rpim(I) all: 0.501 / Rrim(I) all: 1.363 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EA4

5ea4


Resolution: 3→46.88 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2289 2522 5.08 %
Rwork0.1975 --
obs0.1991 49606 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.33 Å2 / Biso mean: 74.9791 Å2 / Biso min: 25.41 Å2
Refinement stepCycle: final / Resolution: 3→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10063 0 187 9 10259
Biso mean--111.51 50.35 -
Num. residues----1298
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6241X-RAY DIFFRACTION5.685TORSIONAL
12B6241X-RAY DIFFRACTION5.685TORSIONAL
13C6241X-RAY DIFFRACTION5.685TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.05770.34241290.292225882717100
3.0577-3.12010.32871510.281125622713100
3.1201-3.18790.29631360.272725822718100
3.1879-3.26210.33831300.262325822712100
3.2621-3.34360.29031470.244925692716100
3.3436-3.4340.26371340.216225892723100
3.434-3.5350.2391380.217125972735100
3.535-3.64910.23991440.204825852729100
3.6491-3.77940.261480.210725862734100
3.7794-3.93070.221480.197225832731100
3.9307-4.10950.25421180.18826212739100
4.1095-4.3260.18661440.165626002744100
4.326-4.59680.18791190.15426312750100
4.5968-4.95140.17221640.150526192783100
4.9514-5.4490.19281620.170826172779100
5.449-6.23590.23581280.19726692797100
6.2359-7.85060.22051390.20326942833100
7.8506-46.89050.21731430.19552810295398

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