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- PDB-6vtw: De novo protein design enables the precise induction of RSV-neutr... -

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Basic information

Entry
Database: PDB / ID: 6vtw
TitleDe novo protein design enables the precise induction of RSV-neutralizing antibodies
Components
  • 101F Fab Heavy Chain
  • 101F Fab Light Chain
  • S4_2.45
KeywordsIMMUNE SYSTEM / de novo designed / immunogens / antibodies / in vivo
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Human respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJardetzky, T. / Correia, B.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation2015/333 Switzerland
European Commission716058European Union
CitationJournal: Science / Year: 2020
Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies.
Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. / Corthesy, P. / Georgeon, S. / Villard, M. / Richard, C.A. / Descamps, D. / Delgado, T. / Oricchio, E. / Rameix-Welti, M.A. / Mas, V. / Ervin, S. / Eleouet, J.F. / Riffault, S. / Bates, J.T. / Julien, J.P. / Li, Y. / Jardetzky, T. / Krey, T. / Correia, B.E.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 10, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S4_2.45
L: 101F Fab Light Chain
H: 101F Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)52,4783
Polymers52,4783
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.224, 148.224, 45.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein/peptide S4_2.45


Mass: 5096.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HEK293-6E cell / Source: (synth.) Human respiratory syncytial virus A2
#2: Antibody 101F Fab Light Chain


Mass: 23952.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293-F cell / Production host: Homo sapiens (human)
#3: Antibody 101F Fab Heavy Chain


Mass: 23428.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK293-F cell / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.02 % / Description: cuboid
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: containing 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate pH 6.5, 20 %(w/v) PEG 8000
PH range: 5.0 - 7.0 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cold N2 stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→37.06 Å / Num. obs: 17472 / % possible obs: 91 % / Redundancy: 6.5 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.07259 / Rpim(I) all: 0.03012 / Rrim(I) all: 0.07879 / Net I/σ(I): 17.14
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.8539 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1567 / CC1/2: 0.116 / CC star: 0.456 / Rpim(I) all: 0.4332 / Rrim(I) all: 0.9625 / % possible all: 89.58

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O41

3o41


Resolution: 2.6→37.06 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 1748 10.01 %
Rwork0.2074 --
obs0.2147 17454 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 0 94 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123769
X-RAY DIFFRACTIONf_angle_d1.9265125
X-RAY DIFFRACTIONf_dihedral_angle_d6.511515
X-RAY DIFFRACTIONf_chiral_restr0.249584
X-RAY DIFFRACTIONf_plane_restr0.017653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.37891420.30841164X-RAY DIFFRACTION89
2.68-2.760.41761370.26731257X-RAY DIFFRACTION96
2.76-2.860.34791440.261314X-RAY DIFFRACTION100
2.86-2.980.37071450.25041308X-RAY DIFFRACTION100
2.98-3.110.32811470.24841304X-RAY DIFFRACTION100
3.11-3.280.32571500.23671316X-RAY DIFFRACTION100
3.28-3.480.32751540.21781324X-RAY DIFFRACTION100
3.48-3.750.28071410.20741324X-RAY DIFFRACTION100
3.75-4.130.24481410.17991336X-RAY DIFFRACTION100
4.13-4.720.20751500.15841312X-RAY DIFFRACTION100
4.72-5.940.26861430.17561356X-RAY DIFFRACTION100
5.95-37.060.26881540.22661391X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -46.2207 Å / Origin y: -37.8662 Å / Origin z: -6.3608 Å
111213212223313233
T0.2952 Å20.0622 Å20.0573 Å2-0.3611 Å20.061 Å2--0.2648 Å2
L2.045 °20.2029 °20.2947 °2-2.1484 °20.486 °2--1.2543 °2
S-0.0069 Å °0.1531 Å °0.1844 Å °-0.0197 Å °0.023 Å °-0.0984 Å °-0.1881 Å °-0.0827 Å °-0.0027 Å °
Refinement TLS groupSelection details: all

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