7Q1R | pdb_00007q1r

A de novo designed homo-dimeric antiparallel coiled coil apCC-Di

• PDB DOI: https://doi.org/10.2210/pdb7Q1R/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2021-10-20 Released: 2022-07-20 
• Deposition Author(s): Shanmugaratnam, S., Rhys, G.G., Dawson, W.M., Woolfson, D.N., Hocker, B.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: other

Literature

De novo designed peptides for cellular delivery and subcellular localisation.

Rhys, G.G., Cross, J.A., Dawson, W.M., Thompson, H.F., Shanmugaratnam, S., Savery, N.J., Dodding, M.P., Hocker, B., Woolfson, D.N.

(2022) Nat Chem Biol 18: 999-1004

• PubMed: 35836017 
• DOI: https://doi.org/10.1038/s41589-022-01076-6
• Primary Citation Related Structures: 
  7Q1Q, 7Q1R, 7Q1S, 7Q1T


• PubMed Abstract: 
  

  Increasingly, it is possible to design peptide and protein assemblies de novo from first principles or computationally. This approach provides new routes to functional synthetic polypeptides, including designs to target and bind proteins of interest. Much of this work has been developed in vitro. Therefore, a challenge is to deliver de novo polypeptides efficiently to sites of action within cells. Here we describe the design, characterisation, intracellular delivery, and subcellular localisation of a de novo synthetic peptide system. This system comprises a dual-function basic peptide, programmed both for cell penetration and target binding, and a complementary acidic peptide that can be fused to proteins of interest and introduced into cells using synthetic DNA. The designs are characterised in vitro using biophysical methods and X-ray crystallography. The utility of the system for delivery into mammalian cells and subcellular targeting is demonstrated by marking organelles and actively engaging functional protein complexes.

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Organizational Affiliation: 
• Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
School of Chemistry, University of Bristol, Bristol, UK.
School of Biochemistry, University of Bristol, Bristol, UK.
BrisSynBio, University of Bristol, Bristol, UK.
Department of Biochemistry, University of Bayreuth, Bayreuth, Germany. [e-mail].
School of Chemistry, University of Bristol, Bristol, UK. [e-mail].
School of Biochemistry, University of Bristol, Bristol, UK. [e-mail].
BrisSynBio, University of Bristol, Bristol, UK. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 6.88 kDa 
• Atom Count: 602 
• Modeled Residue Count: 63 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
apCC-Di	A, B	32	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	C [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.096	α = 90
b = 35.096	β = 90
c = 92.433	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Shanmugaratnam, S., Rhys, G.G., Dawson, W.M., Woolfson, D.N., Hocker, B.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	888993

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2022-07-27
  Changes: Database references
• Version 1.2: 2022-08-31
  Changes: Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary