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- PDB-5tok: Crystal structure of the RSV F glycoprotein in complex with the n... -

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Basic information

Entry
Database: PDB / ID: 5tok
TitleCrystal structure of the RSV F glycoprotein in complex with the neutralizing single-domain antibody F-VHH-L66
Components
  • Fusion glycoprotein F0, Fibritin chimera
  • Single-domain antibody F-VHH-L66
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Fusion / nanobody / immunoglobulin fold / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsGilman, M.S.A. / Kabeche, S.C. / McLellan, J.S.
Funding support United States, Belgium, Spain, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
IWT-VlaanderenPh.D. Student Fellowship Belgium
FWO-VlaanderenPostdoctoral Fellowship Belgium
Ghent UniversityBOF12/GOA/014 Belgium
Interuniversity Attraction Poles ProgramIAP7, BELVIR Belgium
VIB and MinecoSAF2015-67033-R Spain
CitationJournal: Nat Commun / Year: 2017
Title: Potent single-domain antibodies that arrest respiratory syncytial virus fusion protein in its prefusion state.
Authors: Rossey, I. / Gilman, M.S. / Kabeche, S.C. / Sedeyn, K. / Wrapp, D. / Kanekiyo, M. / Chen, M. / Mas, V. / Spitaels, J. / Melero, J.A. / Graham, B.S. / Schepens, B. / McLellan, J.S. / Saelens, X.
History
DepositionOct 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Experimental preparation
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 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 1.6Oct 4, 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
A: Fusion glycoprotein F0, Fibritin chimera
B: Fusion glycoprotein F0, Fibritin chimera
C: Fusion glycoprotein F0, Fibritin chimera
D: Single-domain antibody F-VHH-L66
E: Single-domain antibody F-VHH-L66
F: Single-domain antibody F-VHH-L66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,96410
Polymers226,2066
Non-polymers7594
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-93 kcal/mol
Surface area71630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.890, 138.890, 221.902
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
12chain D
22chain E
32chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA27 - 800
211chain BB27 - 800
311chain CC27 - 800
112chain DD1 - 111
212chain EE2 - 115
312chain FF1 - 111

NCS ensembles :
ID
1
2

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Components

#1: Protein Fusion glycoprotein F0, Fibritin chimera / Protein F


Mass: 61045.008 Da / Num. of mol.: 3 / Mutation: S155C, S190F, V207L, S290C, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Antibody Single-domain antibody F-VHH-L66


Mass: 14356.897 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Komagataella pastoris GS115 (fungus)
#3: 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.: 3
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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: 4.79 mg/mL EndoH-digested DS-Cav1 + F-VHH-L66, 0.05 M potassium phosphate, 20% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.8→50.38 Å / Num. obs: 25035 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 95.53 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.332 / Rpim(I) all: 0.157 / Rrim(I) all: 0.368 / Net I/σ(I): 5.2 / Num. measured all: 133629 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.8-4.065.51.2462458144570.5490.5811.3781.5100
10.75-50.384.80.054572412050.9970.0270.0618.698.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.23data scaling
PDB_EXTRACT3.2data extraction
MOSFLM7.2.0data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Prefusion F (PDB entry 4MMS) and unbound F-VHH-4 structure

4mms


Resolution: 3.8→50.376 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2858 1205 4.82 %
Rwork0.2475 23776 -
obs0.2494 24981 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 324.3 Å2 / Biso mean: 124.023 Å2 / Biso min: 39.73 Å2
Refinement stepCycle: final / Resolution: 3.8→50.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13952 0 47 0 13999
Biso mean--121.16 --
Num. residues----1806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714268
X-RAY DIFFRACTIONf_angle_d1.12719294
X-RAY DIFFRACTIONf_chiral_restr0.0482259
X-RAY DIFFRACTIONf_plane_restr0.0052440
X-RAY DIFFRACTIONf_dihedral_angle_d12.5095190
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6698X-RAY DIFFRACTION6.846TORSIONAL
12B6698X-RAY DIFFRACTION6.846TORSIONAL
13C6698X-RAY DIFFRACTION6.846TORSIONAL
21D1677X-RAY DIFFRACTION6.846TORSIONAL
22E1677X-RAY DIFFRACTION6.846TORSIONAL
23F1677X-RAY DIFFRACTION6.846TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.95210.42531270.333225992726100
3.9521-4.13190.34481430.295225832726100
4.1319-4.34960.28151460.272326092755100
4.3496-4.6220.24721090.253226242733100
4.622-4.97860.31291330.249926082741100
4.9786-5.4790.29491250.250126622787100
5.479-6.27060.33681240.257326422766100
6.2706-7.89540.29041400.245726822822100
7.8954-50.38020.2141580.19032767292599
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)
12.11590.6058-0.73541.5520.20851.2656-0.00381.15090.3846-0.35480.16270.1377-0.1003-1.2012-0.2780.6640.2241-0.00891.96420.29290.7589-11.131635.7315-27.5052
23.00640.51662.38380.92171.52328.99950.017-0.02780.5998-0.0862-0.13210.1666-0.627-0.41170.05980.95710.02290.20610.53640.07590.7577-6.39937.759434.1308
33.0849-0.915-0.4632.5020.05891.8170.27121.13880.6323-0.29290.02970.4548-0.7612-1.0466-0.05210.97210.43940.19821.59740.57671.0608-9.908157.083-26.1217
40.50790.434-1.1634-0.09060.29646.20150.3980.00120.1538-0.1013-0.03970.185-0.37360.3304-0.43920.97630.07550.17640.73140.02110.88184.187741.092532.1924
51.7610.379-0.51913.04130.49861.71290.11741.17490.4839-0.48540.23760.3419-0.3447-1.3123-0.30560.79770.3390.0942.38110.63651.1831-28.498646.7598-23.383
63.8408-2.673.45541.3755-3.62835.86630.53330.31930.5261-0.1063-0.34640.0559-0.1909-0.0104-0.17131.2970.06220.32680.8343-0.051.2014-6.186349.631831.3372
73.8691.6662-0.62526.0091-0.33483.55030.33640.60461.4219-0.2178-0.4980.4376-0.19190.41230.16091.42290.41870.17781.24450.36791.7487-5.351689.6448-21.9817
86.9546-2.9801-1.6586.22212.5396.35-0.38230.0759-0.3093-0.05360.28760.00030.5155-0.91750.09090.6638-0.16780.11540.80910.04380.548615.001616.7598-33.0061
93.66560.33571.26041.6175-0.31540.9263-0.39780.4191-0.68870.01320.30760.7766-0.6981-0.61560.04780.61730.02330.06743.48230.24981.5051-57.137533.2225-15.4404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:472)A27 - 472
2X-RAY DIFFRACTION2(chain A and resid 473:547)A473 - 547
3X-RAY DIFFRACTION3(chain B and resid 27:472)B27 - 472
4X-RAY DIFFRACTION4(chain B and resid 473:549)B473 - 549
5X-RAY DIFFRACTION5(chain C and resid 27:466)C27 - 466
6X-RAY DIFFRACTION6(chain C and resid 467:545)C467 - 545
7X-RAY DIFFRACTION7(chain D and resid 1:114)D1 - 114
8X-RAY DIFFRACTION8(chain E and resid 1:111)E1 - 111
9X-RAY DIFFRACTION9(chain F and resid 1:113)F1 - 113

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