8FRF | pdb_00008frf

Homodimeric designed loop protein RBL7_C2_3

• PDB DOI: https://doi.org/10.2210/pdb8FRF/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-06 Released: 2024-04-17 
• Deposition Author(s): Jude, K.M., Jiang, H., Baker, D., Garcia, K.C.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: in silico

Literature

De novo design of buttressed loops for sculpting protein functions.

Jiang, H., Jude, K.M., Wu, K., Fallas, J., Ueda, G., Brunette, T.J., Hicks, D.R., Pyles, H., Yang, A., Carter, L., Lamb, M., Li, X., Levine, P.M., Stewart, L., Garcia, K.C., Baker, D.

(2024) Nat Chem Biol 20: 974-980

• PubMed: 38816644 
• DOI: https://doi.org/10.1038/s41589-024-01632-2
• Primary Citation Related Structures: 
  8FRE, 8FRF


• PubMed Abstract: 
  

  In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9-14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 187.19 kDa 
• Atom Count: 12,376 
• Modeled Residue Count: 1,648 
• Deposited Residue Count: 1,736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RBL7_C2_3	A, B, C, D, E, F, G, H	217	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	I [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/981

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.961	α = 90
b = 117.644	β = 90
c = 142.056	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Jude, K.M., Jiang, H., Baker, D., Garcia, K.C.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-06-26
  Changes: Database references
• Version 1.2: 2024-08-07
  Changes: Database references