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- PDB-9f90: Crystal structure of a designed three-motif Respiratory Syncytial... -

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Basic information

Entry
Database: PDB / ID: 9f90
TitleCrystal structure of a designed three-motif Respiratory Syncytial Virus immunogen in complex with motavizumab fab
Components
  • Motavizumab Fab heavy chain
  • Motavizumab Fab light chain
  • RSVF-multi-epitope designed scaffold
KeywordsDE NOVO PROTEIN / Designed immunogen / Specific Binding / RSV F protein
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsCastro, K.M. / Correia, B.E.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning
Authors: Castro, K.M. / Watson, J.L. / Wang, J. / Southern, J. / Ayardulabi, R. / Georgeon, S. / Rosset, S. / Baker, D. / Correia, B.E.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Motavizumab Fab light chain
A: Motavizumab Fab heavy chain
C: Motavizumab Fab light chain
D: Motavizumab Fab heavy chain
H: RSVF-multi-epitope designed scaffold
G: RSVF-multi-epitope designed scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,68910
Polymers126,5326
Non-polymers1564
Water81145
1
B: Motavizumab Fab light chain
A: Motavizumab Fab heavy chain
H: RSVF-multi-epitope designed scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3836
Polymers63,2663
Non-polymers1173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Motavizumab Fab light chain
D: Motavizumab Fab heavy chain
G: RSVF-multi-epitope designed scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3054
Polymers63,2663
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.072, 66.859, 109.410
Angle α, β, γ (deg.)90.000, 103.870, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-301-

K

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Components

#1: Antibody Motavizumab Fab light chain


Mass: 23104.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Motavizumab Fab heavy chain


Mass: 24284.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein RSVF-multi-epitope designed scaffold


Mass: 15877.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 0.1 M sodium cacodylate pH 6.5, and 10 % (v/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873129 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873129 Å / Relative weight: 1
ReflectionResolution: 2.907→89.35 Å / Num. obs: 28710 / % possible obs: 99.67 % / Redundancy: 3.03 % / Biso Wilson estimate: 45.57 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.14
Reflection shellResolution: 2.91→3.014 Å / Num. unique obs: 2829 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→61.5 Å / SU ML: 0.3607 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2622 1411 4.92 %
Rwork0.2243 27268 -
obs0.2262 28679 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.42 Å2
Refinement stepCycle: LAST / Resolution: 2.91→61.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8238 0 4 45 8287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078428
X-RAY DIFFRACTIONf_angle_d1.08111473
X-RAY DIFFRACTIONf_chiral_restr0.06441327
X-RAY DIFFRACTIONf_plane_restr0.00831452
X-RAY DIFFRACTIONf_dihedral_angle_d15.60612994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.010.36491450.3242692X-RAY DIFFRACTION99.82
3.01-3.130.33391360.30892712X-RAY DIFFRACTION99.68
3.13-3.270.33251370.29362699X-RAY DIFFRACTION99.82
3.27-3.450.30151420.25082697X-RAY DIFFRACTION99.72
3.45-3.660.27311440.23222733X-RAY DIFFRACTION99.62
3.66-3.940.25231510.22382701X-RAY DIFFRACTION99.89
3.95-4.340.25271360.19672719X-RAY DIFFRACTION100
4.34-4.970.23341370.16842756X-RAY DIFFRACTION99.83
4.97-6.260.21081440.19942743X-RAY DIFFRACTION99.65
6.26-61.50.2271390.20652816X-RAY DIFFRACTION98.83

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