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- PDB-9ra5: Respiratory syncytial virus fusion protein N-terminal heptad repe... -

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Basic information

Entry
Database: PDB / ID: 9ra5
TitleRespiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex with Double stapled peptide 3/4i
Components
  • Double stapled peptide 3/4i
  • Fusion glycoprotein F1
KeywordsANTIVIRAL PROTEIN / Human Respiratory Syncytial Virus / Fusion Protein / Fusion Inhibitor / Stapled Peptide / Six Helix Bundle / Complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma 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 A
human respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.625 Å
AuthorsDuquerroy, S. / Nyanguile, O. / Gsponer, N. / Nicolet, N. / Marti, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Other governmentHES-SO 78166/IA-INTERDISC17-2 Switzerland
Citation
Journal: To Be Published
Title: Double stapled peptide scan yields 3/4i, a potent fusion inhibitor of Respiratory Syncytial Virus
Authors: Gsponer, N. / Nicolet, N. / Marti, R. / Duquerroy, S. / Nyanguile, O.
#1: Journal: Antimicrob Agents Chemother / Year: 2017
Title: A Short Double-Stapled Peptide Inhibits Respiratory Syncytial Virus Entry and Spreading.
Authors: Gaillard, V. / Galloux, M. / Garcin, D. / Eleouet, J.F. / Le Goffic, R. / Larcher, T. / Rameix-Welti, M.A. / Boukadiri, A. / Heritier, J. / Segura, J.M. / Baechler, E. / Arrell, M. / Mottet- ...Authors: Gaillard, V. / Galloux, M. / Garcin, D. / Eleouet, J.F. / Le Goffic, R. / Larcher, T. / Rameix-Welti, M.A. / Boukadiri, A. / Heritier, J. / Segura, J.M. / Baechler, E. / Arrell, M. / Mottet-Osman, G. / Nyanguile, O.
History
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F1
D: Double stapled peptide 3/4i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0444
Polymers7,9122
Non-polymers1312
Water64936
1
A: Fusion glycoprotein F1
D: Double stapled peptide 3/4i
hetero molecules

A: Fusion glycoprotein F1
D: Double stapled peptide 3/4i
hetero molecules

A: Fusion glycoprotein F1
D: Double stapled peptide 3/4i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,13112
Polymers23,7376
Non-polymers3946
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12140 Å2
ΔGint-96 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.32, 78.32, 78.32
Angle α, β, γ (deg.)90, 90, 90
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Fusion glycoprotein F1 / F1


Mass: 5564.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptides were synthesized by Fmoc/tBu solid-phase peptide chemistry on a Rink Amide AM resin
Source: (synth.) Human respiratory syncytial virus A / References: UniProt: P03420
#2: Protein/peptide Double stapled peptide 3/4i


Mass: 2347.857 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptides were synthesized by Fmoc/tBu solid-phase peptide chemistry
Source: (synth.) human respiratory syncytial virus
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 48.5 % / Description: cubic
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.01M MgCl2 0.05M KCl 15% PEG6000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980111 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2022
RadiationMonochromator: Monochromateur "channel-cut" / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980111 Å / Relative weight: 1
ReflectionResolution: 1.625→20 Å / Num. obs: 10226 / % possible obs: 100 % / Redundancy: 40.1 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.011 / Rrim(I) all: 0.069 / Net I/σ(I): 27
Reflection shellResolution: 1.625→1.65 Å / Redundancy: 41.2 % / Rmerge(I) obs: 6.572 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 533 / CC1/2: 0.298 / CC star: 0.671 / Rpim(I) all: 1.035 / Rrim(I) all: 6.653 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSBUILT 20250327data reduction
Aimless0.8.2data scaling
PHASERphasing
autoPROC1.0.5data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.625→14.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.974 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.085 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 496 -RANDOM
Rwork0.1934 ---
obs0.1941 10211 99.9 %-
Displacement parametersBiso mean: 69.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.625→14.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 7 36 554
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011100HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.862016HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d354SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes173HARMONIC5
X-RAY DIFFRACTIONt_it536HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion73SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1064SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion17.54
LS refinement shellResolution: 1.625→1.65 Å
RfactorNum. reflection% reflection
Rfree0.3258 14 -
Rwork0.3143 --
obs--99.55 %
Refinement TLS params.

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)
19.64673.44444.86625.75712.972910.2070.05070.1898-0.30530.1898-0.04590.4439-0.30530.4439-0.0048-0.1059-0.0026-0.0003-0.11080.0035-0.1111-2.1775-7.0862-9.5949
211.75584.44252.185711.4146-0.55268.58770.0812-0.37180.0598-0.3718-0.01810.0410.05980.041-0.063-0.09090.0263-0.0092-0.10490.0362-0.1812-10.2036-4.9167-19.8517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A158 - 203
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ D|* }D496 - 497
4X-RAY DIFFRACTION2{ D|* }D498
5X-RAY DIFFRACTION2{ D|* }D499 - 500
6X-RAY DIFFRACTION2{ D|* }D501
7X-RAY DIFFRACTION2{ D|* }D502 - 506
8X-RAY DIFFRACTION2{ D|* }D507
9X-RAY DIFFRACTION2{ D|* }D508 - 510
10X-RAY DIFFRACTION2{ D|* }D511
11X-RAY DIFFRACTION2{ D|* }D512 - 517

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