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- PDB-29qj: Respiratory syncytial virus fusion protein N-terminal heptad repe... -

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Basic information

Entry
Database: PDB / ID: 29qj
TitleRespiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex with Double stapled peptide 4/4g
Components
  • Double stapled peptide 4/4g
  • Fusion glycoprotein F1
KeywordsVIRAL PROTEIN / Human Respiratory Syncytial Virus / Fusion Protein / Fusion Inhibitor / Stapled Peptide / Six Helix Bundle / Complex / ANTIVIRAL PROTEIN
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: 1.325 Å
AuthorsDuquerroy, S. / Nyanguile, O. / Gsponer, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Other governmentHES-SO 78166/IA-INTERDISC17-2 Switzerland
Citation
Journal: J.Med.Chem. / Year: 2026
Title: Double-Stapled Peptide Scan Yields Potent Fusion Inhibitors of Respiratory Syncytial Virus.
Authors: Pidoux, N. / Roh, L. / Nicolet, N. / Marti, R. / Le Rouzic, A. / Prompt, C. / Fix, J. / Duquerroy, S. / Rey, F. / Rameix-Welti, M.A. / Keck, M. / Barbe, P. / Garcin, D. / Mottet-Osman, G. / ...Authors: Pidoux, N. / Roh, L. / Nicolet, N. / Marti, R. / Le Rouzic, A. / Prompt, C. / Fix, J. / Duquerroy, S. / Rey, F. / Rameix-Welti, M.A. / Keck, M. / Barbe, P. / Garcin, D. / Mottet-Osman, G. / Larcher, T. / Galloux, M. / 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
DepositionMar 30, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F1
D: Double stapled peptide 4/4g


Theoretical massNumber of molelcules
Total (without water)8,0282
Polymers8,0282
Non-polymers00
Water84747
1
A: Fusion glycoprotein F1
D: Double stapled peptide 4/4g

A: Fusion glycoprotein F1
D: Double stapled peptide 4/4g

A: Fusion glycoprotein F1
D: Double stapled peptide 4/4g


Theoretical massNumber of molelcules
Total (without water)24,0856
Polymers24,0856
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10120 Å2
ΔGint-98 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.083, 41.083, 200.844
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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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 4/4g


Mass: 2463.955 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.8 Å3/Da / Density % sol: 39.7 % / Description: trapeze
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350 0.2M NH4I

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Data collection

DiffractionMean temperature: 95 K / Ambient temp details: nitrogen-flow cooling / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2006
RadiationMonochromator: channel cut monochromator made from a Si(111) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.325→67 Å / Num. obs: 12173 / % possible obs: 77.3 % / Redundancy: 19.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.017 / Rrim(I) all: 0.075 / Net I/σ(I): 18
Reflection shellResolution: 1.325→1.432 Å / Redundancy: 19.5 % / Rmerge(I) obs: 2.258 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 609 / CC1/2: 0.66 / Rpim(I) all: 0.522 / Rrim(I) all: 2.319 / % possible all: 19.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC20250717data processing
Aimless0.8.2data scaling
PHASER2.8.3phasing
XDSJan 19, 2025 (BUILT 20251103)data scaling
STARANISO3.0.12 (20250608)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.325→14.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 612 -RANDOM
Rwork0.2049 11540 --
obs0.2062 12152 77.3 %-
Displacement parametersBiso mean: 30.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.7166 Å20 Å20 Å2
2---0.7166 Å20 Å2
3---1.4331 Å2
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: LAST / Resolution: 1.325→14.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms523 0 0 47 570
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.22213HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d395SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes195HARMONIC5
X-RAY DIFFRACTIONt_it581HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion81SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1252SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion19.04
LS refinement shellResolution: 1.325→1.41 Å
RfactorNum. reflection% reflection
Rfree0.3267 27 -
Rwork0.2747 379 -
obs--15.4 %
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)
10.9758-0.3273-0.85410.92991.44734.6668-0.0529-0.2513-0.01950.21740.01550.0930.3038-0.01860.03740.0461-0.0020.04310.04970.00210.014-3.142119.493986.467
22.8634-0.52610.34911.7932-0.19895.6867-0.04960.0709-0.31850.1287-0.0322-0.2140.20280.23280.0817-0.0210.0146-0.0053-0.03460.00820.04216.351315.025676.2926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A158 - 206
2X-RAY DIFFRACTION2{ D|* }D496 - 499
3X-RAY DIFFRACTION2{ D|* }D500
4X-RAY DIFFRACTION2{ D|* }D501 - 503
5X-RAY DIFFRACTION2{ D|* }D504
6X-RAY DIFFRACTION2{ D|* }D505 - 507
7X-RAY DIFFRACTION2{ D|* }D508
8X-RAY DIFFRACTION2{ D|* }D509 - 511
9X-RAY DIFFRACTION2{ D|* }D512
10X-RAY DIFFRACTION2{ D|* }D513 - 514

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