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

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Basic information

Entry
Database: PDB / ID: 5toj
TitleCrystal structure of the RSV F glycoprotein in complex with the neutralizing single-domain antibody F-VHH-4
Components
  • Fusion glycoprotein F0, Fibritin chimera
  • Single-domain antibody F-VHH-4
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 / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 / 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, Fibritin chimera
B: Fusion glycoprotein F0, Fibritin chimera
C: Fusion glycoprotein F0, Fibritin chimera
D: Single-domain antibody F-VHH-4
E: Single-domain antibody F-VHH-4
F: Single-domain antibody F-VHH-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,1109
Polymers226,4466
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24220 Å2
ΔGint-84 kcal/mol
Surface area71400 Å2
Unit cell
Length a, b, c (Å)173.189, 173.189, 153.301
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
12chain D
22chain E
32chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNNAGNAGchain AAA - G27 - 80027
21ASNASNNAGNAGchain BBB - H27 - 80027
31ASNASNNAGNAGchain CCC - I27 - 80027
12GLNGLNHISHISchain DDD1 - 1141 - 126
22GLNGLNVALVALchain EEE1 - 1111 - 123
32GLNGLNSERSERchain FFF1 - 1131 - 125

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-4


Mass: 14436.960 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


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

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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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.45 mg/mL EndoH-digested DS-Cav1 + F-VHH-4, 14.75% w/v PEG3350, 8.8% v/v isopropanol, 0.2 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→37.96 Å / Num. obs: 40311 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 85.08 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.073 / Rrim(I) all: 0.202 / Net I/σ(I): 9.2 / Num. measured all: 299347 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.437.51.0813345144770.5450.4151.1592.1100
11.9-37.966.60.0461669310.9990.0160.04324.997.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.23data scaling
PDB_EXTRACT3.2data extraction
iMOSFLM7.2.0data reduction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Prefusion F (PDB entry 4MMS) and unbound F-VHH-4 structure

4mms


Resolution: 3.3→37.956 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 2022 5.02 %
Rwork0.1841 38255 -
obs0.1866 40277 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 279.97 Å2 / Biso mean: 94.5094 Å2 / Biso min: 40.68 Å2
Refinement stepCycle: final / Resolution: 3.3→37.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14082 0 42 0 14124
Biso mean--97.31 --
Num. residues----1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514399
X-RAY DIFFRACTIONf_angle_d1.19519472
X-RAY DIFFRACTIONf_chiral_restr0.0482271
X-RAY DIFFRACTIONf_plane_restr0.0052461
X-RAY DIFFRACTIONf_dihedral_angle_d13.3755251
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6807X-RAY DIFFRACTION8.792TORSIONAL
12B6807X-RAY DIFFRACTION8.792TORSIONAL
13C6807X-RAY DIFFRACTION8.792TORSIONAL
21D1700X-RAY DIFFRACTION8.792TORSIONAL
22E1700X-RAY DIFFRACTION8.792TORSIONAL
23F1700X-RAY DIFFRACTION8.792TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3001-3.38260.29521430.287826782821
3.3826-3.47390.32911590.266726962855
3.4739-3.57610.28141530.249726862839
3.5761-3.69140.34161470.240126912838
3.6914-3.82330.26471370.222127112848
3.8233-3.97620.24511390.207627122851
3.9762-4.15690.21161460.185727242870
4.1569-4.37580.1971510.157527272878
4.3758-4.64950.2081460.150827042850
4.6495-5.00770.22421140.148727592873
5.0077-5.51030.22181590.162727312890
5.5103-6.30450.21121510.175627512902
6.3045-7.93110.22361440.179727902934
7.9311-37.95850.20681330.1628953028
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)
11.45550.43530.00982.50840.01841.20580.161-0.0316-0.2758-0.0816-0.06330.31630.1804-0.47-0.07640.4360.0399-0.09940.81390.03610.54468.8104-58.7656172.2283
24.46120.81332.6434-0.14520.14091.23150.02160.3889-0.003-0.03120.0588-0.0932-0.25330.2059-0.03890.6172-0.11270.05070.7318-0.07050.469658.2661-34.1903186.7312
32.23540.07350.97081.39520.12132.99890.27360.5652-0.4872-0.6016-0.10790.31830.338-0.4052-0.26530.72120.0693-0.21750.8057-0.1730.738317.835-72.0342152.8124
43.08441.58551.4650.68880.96560.51180.10890.1248-0.2624-0.01740.0428-0.1267-0.13690.0447-0.15670.568-0.131-0.12180.7530.06340.646345.2323-57.0151191.0897
52.6984-0.4007-0.15451.12510.02061.22120.21250.2837-0.2188-0.2464-0.10090.3137-0.016-0.2983-0.1310.62010.1866-0.11740.793-0.05240.477217.3809-51.9279154.2067
62.80682.6594.13322.44074.07457.94630.16-0.24410.03290.05740.0539-0.09050.0177-0.2372-0.24170.4196-0.10380.04350.47280.04910.469875.1672-40.1959191.2998
73.05021.9493-3.66064.6284-3.79635.2378-0.07930.2789-0.02280.22770.13820.1805-0.2564-0.0768-0.03250.3786-0.0804-0.0610.8963-0.09620.567-1.1805-64.3819202.8631
83.11870.4891-3.00675.83352.44734.4328-0.22730.6576-1.0817-0.9270.2742-0.06641.15740.3242-0.05961.37690.2465-0.34080.8088-0.38841.23238.6033-93.002144.5092
96.2639-3.99653.77526.6198-2.2165.35520.33830.49030.2155-0.4014-0.33810.0862-0.8973-0.4028-0.04850.96790.36560.07540.91540.0410.504711.5632-21.3871141.6083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:461)A27 - 461
2X-RAY DIFFRACTION2(chain A and resid 462:544)A462 - 544
3X-RAY DIFFRACTION3(chain B and resid 27:383)B27 - 383
4X-RAY DIFFRACTION4(chain B and resid 384:544)B384 - 544
5X-RAY DIFFRACTION5(chain C and resid 27:493)C27 - 493
6X-RAY DIFFRACTION6(chain C and resid 494:544)C494 - 544
7X-RAY DIFFRACTION7(chain D and resid 1:111)D1 - 111
8X-RAY DIFFRACTION8(chain E and resid 2:115)E2 - 115
9X-RAY DIFFRACTION9(chain F and resid 1:111)F1 - 111

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