3F87 | pdb_00003f87

An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Core and a Distinctive Quarternary Structure: GCN4pLI derivative with beta residues at a and d heptad positions - higher symmetry crystal

• PDB DOI: https://doi.org/10.2210/pdb3F87/pdb

• Classification: UNKNOWN FUNCTION
• Mutation(s): No 


• Deposited: 2008-11-11 Released: 2009-07-21 
• Deposition Author(s): Giuliano, M.W., Horne, W.S., Gellman, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.296 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

An alpha/beta-peptide helix bundle with a pure beta3-amino acid core and a distinctive quaternary structure.

Giuliano, M.W., Horne, W.S., Gellman, S.H.

(2009) J Am Chem Soc 131: 9860-9861

• PubMed: 19580264 
• DOI: https://doi.org/10.1021/ja8099294
• Primary Citation Related Structures: 
  3F86, 3F87


• PubMed Abstract: 
  

  Helix bundles are among the most widely studied tertiary and quaternary structural motifs in proteins. Here we present the crystal structure of an alpha/beta-peptide foldamer that adopts a tetrameric helix-bundle quaternary structure with a hydrophobic core composed solely of beta-amino acids. The structure displays features that are unprecedented among all known helix bundles composed of either alpha-peptides or peptidic foldamers. The tetramer is characterized by an asymmetry of interaction between neighboring helices, and the side-chain packing within the hydrophobic core differs fundamentally from the knobs-into-holes arrangement typical of most helix bundles.

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Organizational Affiliation: 
• Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.99 kDa 
• Atom Count: 1,298 
• Modeled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4pLI-betaAD	A, B, C, D	34	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3L	A, B, C, D	L-PEPTIDE LINKING	C7 H15 N O2		--
B3M	A, B, C, D	L-PEPTIDE LINKING	C6 H13 N O2 S		--
BIL	A, B, C, D	L-PEPTIDE LINKING	C7 H15 N O2		--
HMR	A, B, C, D	L-PEPTIDE LINKING	C7 H16 N4 O2		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.296 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.313	α = 90
b = 71.313	β = 90
c = 97.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Giuliano, M.W., Horne, W.S., Gellman, S.H.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations