8DA5 | pdb_00008da5

Coevolved affibody-Z domain pair LL1.c4

• PDB DOI: https://doi.org/10.2210/pdb8DA5/pdb

• Classification: PROTEIN BINDING
• Organism(s): Staphylococcus aureus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-06-13 Released: 2023-07-26 
• Deposition Author(s): Jude, K.M., Yang, A., Garcia, K.C.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), The G. Harold and Leila Y. Mathers Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.

Yang, A., Jude, K.M., Lai, B., Minot, M., Kocyla, A.M., Glassman, C.R., Nishimiya, D., Kim, Y.S., Reddy, S.T., Khan, A.A., Garcia, K.C.

(2023) Science 381: eadh1720-eadh1720

• PubMed: 37499032 
• DOI: https://doi.org/10.1126/science.adh1720
• Primary Citation Related Structures: 
  8DA3, 8DA4, 8DA5, 8DA6, 8DA7, 8DA8, 8DA9, 8DAA, 8DAB, 8DAC


• PubMed Abstract: 
  

  Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Toyota Technological Institute at Chicago, Chicago, IL 60637, USA.
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Departments of Pathology and Family Medicine, University of Chicago, Chicago, IL 60637, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry, gel filtration, surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry, gel filtration, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 31.34 kDa 
• Atom Count: 2,336 
• Modeled Residue Count: 236 
• Deposited Residue Count: 268 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein A	A	67	Staphylococcus aureus	Mutation(s): 4  Gene Names: spa
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein A	B [auth C]	67	Staphylococcus aureus	Mutation(s): 4  Gene Names: spa
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
affibody LL1.FIVM	C [auth B]	67	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
affibody LL1.FIVM	D	67	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LAL	A	L-PEPTIDE LINKING	C5 H11 N O2		ALA
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/922

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.612	α = 90
b = 41.153	β = 90
c = 160.108	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	refinement
BUSTER	refinement
XDS	data reduction
PHASER	phasing
DIALS	data scaling
DIALS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Jude, K.M., Yang, A., Garcia, K.C.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
The G. Harold and Leila Y. Mathers Foundation	United States	MF-1802-00128

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2023-08-09
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Structure summary
• Version 1.3: 2026-03-04
  Changes: Refinement description, Structure summary