5U5C | pdb_00005u5c

Coiled Coil Peptide Metal Coordination Framework: Tetramer Fold

• PDB DOI: https://doi.org/10.2210/pdb5U5C/pdb

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


• Deposited: 2016-12-06 Released: 2017-02-22 
• Deposition Author(s): Tavenor, N.A., Murnin, M.J., Horne, W.S.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.276 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.265 (DCC) 
• R-Value Observed: 
  0.265 (Depositor) 

Starting Model: experimental

Literature

Supramolecular Metal-Coordination Polymers, Nets, and Frameworks from Synthetic Coiled-Coil Peptides.

Tavenor, N.A., Murnin, M.J., Horne, W.S.

(2017) J Am Chem Soc 139: 2212-2215

• PubMed: 28161945 
• DOI: https://doi.org/10.1021/jacs.7b00651
• Primary Citation Related Structures: 
  5U59, 5U5A, 5U5B, 5U5C


• PubMed Abstract: 
  

  Metal coordination and peptide-directed self-assembly are two proven methods for creating defined supramolecular architectures. Here, we report a new class of crystalline materials based on coiled-coil peptides bearing unnatural metal-chelating terpyridine moieties. High-resolution structural characterization of lattices formed in the presence of Cu ²⁺ reveals a general assembly mechanism. Subtle sequence variation in the modular synthetic ligand dictates assembly morphology.

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Organizational Affiliation: 
• Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 20.38 kDa 
• Atom Count: 1,579 
• Modeled Residue Count: 180 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed tetrameric coiled coil peptide with one terpyridine side chain	A, B, C, D, E, F	30	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	I [auth C], N [auth E]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
CU	G [auth B], H [auth C], J [auth D], K [auth E], L [auth E], M [auth E]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.276 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.265 (DCC) 
• R-Value Observed: 0.265 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.297	α = 90
b = 38.642	β = 90
c = 44.198	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Tavenor, N.A., Murnin, M.J., Horne, W.S.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMR1149067

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Structure summary