Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 20.44 kDa 
• Atom Count: 1652 
• Modelled Residue Count: 170 
• Deposited Residue Count: 178 
• Unique protein chains: 2

4A1U

Crystal structure of alpha-beta-foldamer 2c in complex with Bcl-xL

• PDB DOI: 10.2210/pdb4A1U/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2011-09-20 Released: 2011-12-28 
• Deposition Author(s): Boersma, M.D., Haase, H.S., Kaufman, K.J., Horne, W.S., Lee, E.F., Clarke, O.B., Smith, B.J., Colman, P.M., Gellman, S.H., Fairlie, W.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.198 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Evaluation of Diverse Alpha/Beta-Backbone Patterns for Functional Alpha-Helix Mimicry: Analogues of the Bim Bh3 Domain.

Boersma, M.D., Haase, H.S., Peterson-Kaufman, K.J., Lee, E.F., Clarke, O.B., Colman, P.M., Smith, B.J., Horne, W.S., Fairlie, W.D., Gellman, S.H.

(2012) J Am Chem Soc 134: 315

• PubMed: 22040025 
• DOI: 10.1021/ja207148m
• Primary Citation of Related Structures:  
  4A1U, 4A1W


• PubMed Abstract: 
  

Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we describe a comprehensive evaluation of diverse α/β-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-x(L) and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All α/β-peptide homologues retain the side-chain sequence of the Bim BH3 domain, but each homologue contains periodic α-residue → β(3)-residue substitutions. Previous work has shown that the ααβαααβ pattern, which aligns the β(3)-residues in a 'stripe' along one side of the helix, can support functional α-helix mimicry, and the results reported here strengthen this conclusion. The present study provides the first evaluation of functional mimicry by ααβ and αααβ patterns, which cause the β(3)-residues to spiral around the helix periphery. We find that the αααβ pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an α/β-peptide bound to Bcl-x(L), affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best αααβ homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 α-peptide.

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Organizational Affiliation: 

Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2-LIKE PROTEIN 1	A	158	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L1, BCL2L, BCLX Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-BETA-FOLDAMER 2C	B	20	synthetic construct	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
PHAROS:  O43521 GTEx:  ENSG00000153094

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3A	B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
B3E	B	L-PEPTIDE LINKING	C6 H11 N O4		GLU
HR7	B	L-PEPTIDE LINKING	C7 H16 N4 O2		ARG
HT7	B	L-PEPTIDE LINKING	C12 H14 N2 O2		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.198 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.706	α = 90
b = 54.706	β = 90
c = 119.168	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-20 
• Released Date: 2011-12-28 
Deposition Author(s): Boersma, M.D., Haase, H.S., Kaufman, K.J., Horne, W.S., Lee, E.F., Clarke, O.B., Smith, B.J., Colman, P.M., Gellman, S.H., Fairlie, W.D.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-01-25
  Changes: Other
• Version 2.0: 2019-04-24
  Changes: Advisory, Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2019-07-10
  Changes: Data collection