9F90 | pdb_00009f90

Crystal structure of a designed three-motif Respiratory Syncytial Virus immunogen in complex with motavizumab fab

• PDB DOI: https://doi.org/10.2210/pdb9F90/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Mus musculus, synthetic construct
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-07 Released: 2025-05-21 
• Deposition Author(s): Castro, K.M., Correia, B.E.
• Funding Organization(s): Swiss National Science Foundation, European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: in silico

Literature

Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning

Castro, K.M., Watson, J.L., Wang, J., Southern, J., Ayardulabi, R., Georgeon, S., Rosset, S., Baker, D., Correia, B.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 126.69 kDa 
• Atom Count: 8,287 
• Modeled Residue Count: 1,077 
• Deposited Residue Count: 1,144 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Motavizumab Fab light chain	A [auth B], C	213	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Motavizumab Fab heavy chain	B [auth A], D	225	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RSVF-multi-epitope designed scaffold	E [auth H], F [auth G]	134	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	G [auth B], H [auth A], I [auth C], J [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.072	α = 90
b = 66.859	β = 103.87
c = 109.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Castro, K.M., Correia, B.E.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release