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- PDB-9f91: Crystal structure of a designed Respiratory Syncytial Virus immun... -

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Basic information

Entry
Database: PDB / ID: 9f91
TitleCrystal structure of a designed Respiratory Syncytial Virus immunogen in complex with RSV90 fab
Components
  • Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab
  • RSV90 Fab heavy chain
  • RSV90 Fab light chain
KeywordsDE NOVO PROTEIN / Designed immunogen / Specific Binding / RSV F protein
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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
E: RSV90 Fab heavy chain
F: RSV90 Fab light chain
A: RSV90 Fab heavy chain
B: RSV90 Fab light chain
I: Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab
J: Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab


Theoretical massNumber of molelcules
Total (without water)118,7306
Polymers118,7306
Non-polymers00
Water77543
1
E: RSV90 Fab heavy chain
F: RSV90 Fab light chain
I: Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab


Theoretical massNumber of molelcules
Total (without water)59,3653
Polymers59,3653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-36 kcal/mol
Surface area23550 Å2
2
A: RSV90 Fab heavy chain
B: RSV90 Fab light chain
J: Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab


Theoretical massNumber of molelcules
Total (without water)59,3653
Polymers59,3653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-37 kcal/mol
Surface area23430 Å2
Unit cell
Length a, b, c (Å)113.390, 137.650, 87.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Antibody RSV90 Fab heavy chain


Mass: 24523.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody RSV90 Fab light chain


Mass: 23590.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab


Mass: 11251.649 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 and 20 % (v/v) PEG Smear High

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→73.83 Å / Num. obs: 52204 / % possible obs: 99.79 % / Redundancy: 6.36 % / Biso Wilson estimate: 52.45 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.58
Reflection shellResolution: 2.43→2.517 Å / Num. unique obs: 5153 / CC1/2: 0.58

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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: 2.43→73.83 Å / SU ML: 0.4174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2866 2632 5.04 %
Rwork0.2508 49584 -
obs0.2526 52204 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.76 Å2
Refinement stepCycle: LAST / Resolution: 2.43→73.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7670 0 0 43 7713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01657830
X-RAY DIFFRACTIONf_angle_d0.752710655
X-RAY DIFFRACTIONf_chiral_restr0.0451226
X-RAY DIFFRACTIONf_plane_restr0.00861361
X-RAY DIFFRACTIONf_dihedral_angle_d12.26862767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.470.45351210.42112589X-RAY DIFFRACTION100
2.47-2.520.46661340.40482571X-RAY DIFFRACTION99.93
2.52-2.570.43051490.37392559X-RAY DIFFRACTION99.78
2.57-2.630.41841290.37352594X-RAY DIFFRACTION100
2.63-2.690.38291160.3512576X-RAY DIFFRACTION99.78
2.69-2.760.3891420.33612596X-RAY DIFFRACTION99.82
2.76-2.830.38321500.32942578X-RAY DIFFRACTION99.96
2.83-2.910.34381310.33072611X-RAY DIFFRACTION100
2.91-3.010.39551370.32192583X-RAY DIFFRACTION99.96
3.01-3.120.33261440.30572578X-RAY DIFFRACTION99.82
3.12-3.240.33121340.29282598X-RAY DIFFRACTION99.24
3.24-3.390.33111520.28062555X-RAY DIFFRACTION99.85
3.39-3.570.33291360.26932623X-RAY DIFFRACTION99.93
3.57-3.790.30781460.26232623X-RAY DIFFRACTION99.96
3.79-4.080.27291330.23552609X-RAY DIFFRACTION99.96
4.08-4.490.23351390.20482630X-RAY DIFFRACTION99.86
4.49-5.140.19911440.18462649X-RAY DIFFRACTION99.86
5.14-6.480.25651360.20912664X-RAY DIFFRACTION98.94
6.48-73.830.21531590.18482798X-RAY DIFFRACTION99.5

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