9F91 | pdb_00009f91

Crystal structure of a designed Respiratory Syncytial Virus immunogen in complex with RSV90 fab

PDB DOI: https://doi.org/10.2210/pdb9F91/pdb

Classification: DE NOVO PROTEIN
Organism(s): Homo sapiens, 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.287 (Depositor), 0.287 (DCC)
R-Value Work:
0.251 (Depositor), 0.251 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 118.73 kDa
Atom Count: 7,713
Modeled Residue Count: 1,014
Deposited Residue Count: 1,084
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RSV90 Fab heavy chain	A [auth E], C [auth A]	228	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RSV90 Fab light chain	B [auth F], D [auth B]	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed single epitope Respiratory Syncytial Virus immunogen in complex with RSV90 fab	E [auth I], F [auth J]	97	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.287 (Depositor), 0.287 (DCC)
R-Value Work: 0.251 (Depositor), 0.251 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.39	α = 90
b = 137.65	β = 90
c = 87.47	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.