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- PDB-6dc3: RSV prefusion F bound to RSD5 Fab -

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Basic information

Entry
Database: PDB / ID: 6dc3
TitleRSV prefusion F bound to RSD5 Fab
Components
  • Fab RSD5-Germline Heavy Chain
  • Fab RSD5-Germline Light Chain
  • RSV fusion glycoprotein
KeywordsIMMUNE SYSTEM / Antibody / Viral glycoprotein / Complex
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / immunoglobulin complex / 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 ...positive regulation of syncytium formation by virus / host cell Golgi membrane / immunoglobulin complex / 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 / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. ...Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Fusion glycoprotein F0 / Ig-like domain-containing protein / IGL@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus A
Human immunodeficiency virus 1
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.501 Å
AuthorsBattles, M.B. / McLellan, J.S. / Jones, H.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: Plos Pathog. / Year: 2019
Title: Alternative conformations of a major antigenic site on RSV F.
Authors: Jones, H.G. / Battles, M.B. / Lin, C.C. / Bianchi, S. / Corti, D. / McLellan, J.S.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 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 1.4Oct 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
H: Fab RSD5-Germline Heavy Chain
L: Fab RSD5-Germline Light Chain
F: RSV fusion glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,18318
Polymers110,4923
Non-polymers1,69115
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-155 kcal/mol
Surface area41520 Å2
Unit cell
Length a, b, c (Å)270.320, 270.320, 270.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Antibody Fab RSD5-Germline Heavy Chain


Mass: 24454.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6N089
#2: Antibody Fab RSD5-Germline Light Chain


Mass: 22819.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8N355
#3: Protein RSV fusion glycoprotein / Protein F


Mass: 63218.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) unidentified (others)
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: 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.: 2 / Source method: obtained synthetically / 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: 7.88 Å3/Da / Density % sol: 84.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Lithium sulfate, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→38.23 Å / Num. obs: 41327 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 126.75 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.053 / Rrim(I) all: 0.117 / Net I/σ(I): 9.7 / Num. measured all: 198500 / Scaling rejects: 205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.644.60.846212662126646560.5280.4480.961.8100
12.62-38.234.30.03538919060.9970.0190.0423.595.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMU, 1DFB, 1MCO

4mmu

1dfb

1mco


Resolution: 3.501→38.229 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 1966 4.76 %
Rwork0.1827 39339 -
obs0.1838 41305 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 315.77 Å2 / Biso mean: 132.1736 Å2 / Biso min: 59.2 Å2
Refinement stepCycle: final / Resolution: 3.501→38.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6797 0 93 0 6890
Biso mean--200.55 --
Num. residues----894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5009-3.58840.33011320.325627932925100
3.5884-3.68540.31581200.292828022922100
3.6854-3.79370.31611720.269927532925100
3.7937-3.9160.28071020.254328512953100
3.916-4.05590.24081220.212927842906100
4.0559-4.2180.19991350.182627892924100
4.218-4.40980.18021520.161528172969100
4.4098-4.64190.16391500.143827732923100
4.6419-4.93210.15331580.139727802938100
4.9321-5.3120.19261440.15328242968100
5.312-5.84490.18911700.171527702940100
5.8449-6.68680.2391140.188228572971100
6.6868-8.40980.21741390.179428613000100
8.4098-38.23130.18191560.16772885304199
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)
15.5984-0.87842.83533.28583.66546.4482-0.3302-0.01140.2324-0.71020.0241-0.01610.90190.78840.27741.6452-0.09440.28681.11820.26230.972766.843834.1334-26.8525
26.4677-1.218-0.784.86072.71513.5855-0.1623-0.7141-1.06220.1431-0.382-0.18931.4431-0.36360.53081.8191-0.11990.24971.26580.29470.907955.320628.1223-17.7053
31.23070.45730.9561.13310.48762.44450.0254-0.1885-0.02330.13660.0324-0.4149-0.08640.1639-0.0710.7039-0.0539-0.07350.8447-0.0850.789676.722659.085265.7306
47.7402-3.7184-3.79215.86181.84189.17890.2985-0.0980.202-0.3005-0.3905-0.2363-0.34451.01040.05480.8706-0.1301-0.10871.15640.12070.626665.627752.06428.5955
55.4181.0190.02016.17480.96229.10040.10911.07890.0999-0.4982-0.10080.2391-0.0349-1.2965-0.10980.82970.0333-0.0311.2293-0.06390.598645.309550.74471.7403
65.28620.95145.23751.1420.61437.8392-0.76040.11580.7881-0.0710.0799-0.0493-0.7659-0.1570.7410.76710.08320.0530.469-0.13040.846564.512357.279849.1959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'H' and resid 115 through 215)H115 - 215
2X-RAY DIFFRACTION2(chain 'L' and resid 108 through 210)L108 - 210
3X-RAY DIFFRACTION3(chain 'F' and resid 137 through 602)F137 - 602
4X-RAY DIFFRACTION4(chain 'H' and resid 1 through 114)H1 - 114
5X-RAY DIFFRACTION5(chain 'L' and resid 1 through 107)L1 - 107
6X-RAY DIFFRACTION6(chain 'F' and resid 27 through 101)F27 - 101

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