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- PDB-6oe5: Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs -

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Basic information

Entry
Database: PDB / ID: 6oe5
TitleSplayed open prefusion RSV F captured by CR9501 and motavizumab Fabs
Components
  • CR9501 Fab Heavy Chain
  • CR9501 Fab Light Chain
  • Fusion glycoprotein F0,Fibritin
  • Motavizumab Fab Heavy Chain
  • Motavizumab Fab Light Chain
KeywordsViral protein/immune system / class I fusion glycoprotein / immunoglobulin / respiratory syncytial virus / trimerization / neutralizing / VIRAL PROTEIN / Viral protein-immune system complex
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 / 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
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Enterobacteria phage T4 (virus)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
CitationJournal: Nat Commun / Year: 2019
Title: Transient opening of trimeric prefusion RSV F proteins.
Authors: Gilman, M.S.A. / Furmanova-Hollenstein, P. / Pascual, G. / B van 't Wout, A. / Langedijk, J.P.M. / McLellan, J.S.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0,Fibritin
B: Motavizumab Fab Heavy Chain
C: Motavizumab Fab Light Chain
H: CR9501 Fab Heavy Chain
L: CR9501 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)156,7305
Polymers156,7305
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Each protomer is likely tethered to two identical protomers via a C-terminal trimerization domain. However, density is not visible for this domain, therefore the assembly ...Evidence: gel filtration, Each protomer is likely tethered to two identical protomers via a C-terminal trimerization domain. However, density is not visible for this domain, therefore the assembly cannot be assumed to be trimeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-58 kcal/mol
Surface area49660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.837, 219.837, 68.811
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Fusion glycoprotein F0,Fibritin / prefusion RSV F / Protein F / Collar protein / Whisker antigen control protein


Mass: 61370.312 Da / Num. of mol.: 1 / Mutation: N67I, S215P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: A2 / Gene: wac / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: P10104
#2: Antibody Motavizumab Fab Heavy Chain


Mass: 24284.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Motavizumab Fab Light Chain


Mass: 23150.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody CR9501 Fab Heavy Chain


Mass: 24367.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody CR9501 Fab Light Chain


Mass: 23557.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4.69 mg/mL prefusion F (PR-DM) + motavizumab Fab + CR9501 Fab, 30% (v/v) PEG400, 0.19 M ammonium sulfate, 3.1% (w/v) PEG8000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.1→43.68 Å / Num. obs: 15219 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 138.17 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.295 / Rpim(I) all: 0.116 / Rrim(I) all: 0.318 / Net I/σ(I): 5.3 / Num. measured all: 110763 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.1-4.587.11.26742990.6070.5051.366100
9.17-43.6870.0714120.9880.0280.07698.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.1data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→43.677 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.86
RfactorNum. reflection% reflection
Rfree0.3057 748 4.92 %
Rwork0.2616 --
obs0.2637 15196 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 308.45 Å2 / Biso mean: 174.2892 Å2 / Biso min: 106.9 Å2
Refinement stepCycle: final / Resolution: 4.1→43.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8527 0 0 0 8527
Num. residues----1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038716
X-RAY DIFFRACTIONf_angle_d0.50111864
X-RAY DIFFRACTIONf_chiral_restr0.0421386
X-RAY DIFFRACTIONf_plane_restr0.0051486
X-RAY DIFFRACTIONf_dihedral_angle_d3.965214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
4.1005-4.41680.38111640.320228403004
4.4168-4.86080.31911380.282428813019
4.8608-5.56290.33341530.264228452998
5.5629-7.0040.29941490.300229143063
7.004-43.67960.27041440.22229683112
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)
16.1919-3.2477-2.12663.73872.181-1.137-0.1606-0.2728-0.05640.42390.4031-0.40290.5184-0.2328-0.24871.77350.0019-0.12531.48990.10180.8575158.43771.3646-46.7085
21.49850.1997-0.06923.02232.93060.8390.6122-0.4385-0.47190.8618-0.52030.14480.23390.13170.01081.7745-0.19630.05961.28060.1991.0729152.05464.4141-48.282
3-0.60830.6218-0.45885.84650.5662-0.80390.39410.0153-0.3034-0.4001-0.2322-1.15920.1749-0.1962-0.1771.86430.14-0.15921.5820.03611.2228168.176441.9669-49.183
45.1959-0.44843.58455.15531.59031.6064-0.98381.07941.9008-0.45490.46990.1019-0.3831-0.38930.41741.6598-0.2262-0.08771.64010.28821.2902146.268855.0409-81.0124
56.6595-1.36854.08646.9771-1.11921.4676-1.00390.50571.292-1.22020.34651.6693-1.26130.7450.48581.9581-0.5952-0.45111.86260.48991.9805126.793740.1921-97.8413
61.44123.47171.69829.66072.73343.2263-0.12540.6125-0.3646-0.20190.4063-0.42570.17130.5842-0.26091.814-0.04640.03271.63140.15661.9816153.962134.1345-77.2564
75.3302-0.9326.94696.80753.37168.89080.96721.3089-0.5846-3.06920.20620.6974-0.0510.3473-0.9882.6303-0.26470.01862.2796-0.02651.4382134.523929.6603-108.6626
85.47954.30513.34343.3925-0.33347.5032-0.8152-0.30760.66491.38351.23710.46760.1113-0.0014-0.60441.58320.04130.17351.3027-0.0851.1347159.7776102.609-33.153
90.3071.87471.40653.25531.0392.36850.258-0.64680.34030.4749-0.27540.7835-0.1706-0.74520.07421.4925-0.05590.40971.4851-0.09581.4565147.7972123.0109-38.939
108.7554-3.97055.22726.3628-6.95095.4599-0.2023-0.1272-0.25120.20120.36090.4877-0.2757-0.2562-0.08511.4543-0.05080.09271.1656-0.22630.7488150.631999.6283-54.4444
117.0438-1.00232.19184.61785.81378.7284-0.5542-0.13420.4036-0.35130.09030.0771-0.5227-0.34270.35281.82560.19270.04251.21780.29691.2775145.1497136.617-53.9878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 44:191)A44 - 191
2X-RAY DIFFRACTION2(chain A and resid 192:295)A192 - 295
3X-RAY DIFFRACTION3(chain A and resid 296:462)A296 - 462
4X-RAY DIFFRACTION4(chain B and resid 1:124)B1 - 124
5X-RAY DIFFRACTION5(chain B and resid 125:213)B125 - 213
6X-RAY DIFFRACTION6(chain C and resid 1:106)C1 - 106
7X-RAY DIFFRACTION7(chain C and resid 107:212)C107 - 212
8X-RAY DIFFRACTION8(chain H and resid 2:80)H2 - 80
9X-RAY DIFFRACTION9(chain H and resid 81:214)H81 - 214
10X-RAY DIFFRACTION10(chain L and resid 1:104)L1 - 104
11X-RAY DIFFRACTION11(chain L and resid 105:212)L105 - 212

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