4TL1 | pdb_00004tl1

GCN4-p1 with mutation to 1-Aminocyclohexanecarboxylic acid at residue 10

• PDB DOI: https://doi.org/10.2210/pdb4TL1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae S288C
• Mutation(s): Yes 


• Deposited: 2014-05-28 Released: 2014-08-06 
• Deposition Author(s): Tavenor, N.A., Silva, K.I., Saxena, S., Horne, W.S.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Origins of Structural Flexibility in Protein-Based Supramolecular Polymers Revealed by DEER Spectroscopy.

Tavenor, N.A., Silva, K.I., Saxena, S., Horne, W.S.

(2014) J Phys Chem B 118: 9881-9889

• PubMed: 25060334 
• DOI: https://doi.org/10.1021/jp505643w
• Primary Citation Related Structures: 
  4TL1


• PubMed Abstract: 
  

  Modular assembly of bio-inspired supramolecular polymers is a powerful technique to develop new soft nanomaterials, and protein folding is a versatile basis for preparing such materials. Previous work demonstrated a significant difference in the physical properties of closely related supramolecular polymers composed of building blocks in which identical coiled-coil-forming peptides are cross-linked by one of two subtly different organic linkers (one flexible and the other rigid). Herein, we investigate the molecular basis for this observation by isolating a single subunit of the supramolecular polymer chain and probing its structure and conformational flexibility by double electron-electron resonance (DEER) spectroscopy. Experimental spin-spin distance distributions for two different labeling sites coupled with molecular dynamics simulations provide insights into how the linker structure impacts chain dynamics in the coiled-coil supramolecular polymer.

---

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

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: 8.11 kDa 
• Atom Count: 642 
• Modeled Residue Count: 69 
• Deposited Residue Count: 70 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General control protein GCN4	A, B	35	Saccharomyces cerevisiae S288C	Mutation(s): 1
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
02K	A, B	PEPTIDE LINKING	C7 H13 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.322	α = 90
b = 30.35	β = 101.68
c = 28.019	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CrystalClear	phasing
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Tavenor, N.A., Silva, K.I., Saxena, S., Horne, W.S.

---

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

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2014-08-20
  Changes: Structure summary
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2019-11-27
  Changes: Author supporting evidence
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-11-20
  Changes: Structure summary