5LVS | pdb_00005lvs

Self-assembled protein-aromatic foldamer complexes with 2:3 and 2:2:1 stoichiometries

• PDB DOI: https://doi.org/10.2210/pdb5LVS/pdb

• Classification: LYASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-14 Released: 2017-03-08 
• Deposition Author(s): Jewginski, M., LANGLOIS D'ESTAINTOT, B., Granier, T., Huc, Y.
• Funding Organization(s): Polish Ministry of Science and Higher Education (Mobility Plus Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.178 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Self-Assembled Protein-Aromatic Foldamer Complexes with 2:3 and 2:2:1 Stoichiometries.

Jewginski, M., Granier, T., Langlois d'Estaintot, B., Fischer, L., Mackereth, C.D., Huc, I.

(2017) J Am Chem Soc 139: 2928-2931

• PubMed: 28170240 
• DOI: https://doi.org/10.1021/jacs.7b00184
• Primary Citation Related Structures: 
  5L3O, 5L6K, 5LVS


• PubMed Abstract: 
  

  The promotion of protein dimerization using the aggregation properties of a protein ligand was explored and shown to produce complexes with unusual stoichiometries. Helical foldamer 2 was synthesized and bound to human carbonic anhydrase (HCA) using a nanomolar active site ligand. Crystal structures show that the hydrophobicity of 2 and interactions of its side chains lead to the formation of an HCA ₂ -2 ₃ complex in which three helices of 2 are stacked, two of them being linked to an HCA molecule. The middle foldamer in the stack can be replaced by alternate sequences 3 or 5. Solution studies by CD and NMR confirm left-handedness of the helical foldamers as well as HCA dimerization.

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Organizational Affiliation: 
• CBMN (UMR5248), Univ. Bordeaux, CNRS, IPB , Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600 Pessac, France.
Department of Organic and Pharmaceutical Technology, Faculty of Chemistry, Wrocław University of Science and Technology , 50-370 Wrocław, Poland.
ARNA (U 1212), Univ. Bordeaux, INSERM , Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600 Pessac, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.2 kDa 
• Atom Count: 5,063 
• Modeled Residue Count: 534 
• Deposited Residue Count: 534 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A, B	259	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	C, D	6	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	E [auth H]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.178 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.73	α = 90
b = 54.81	β = 112.77
c = 84.7	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Jewginski, M., LANGLOIS D'ESTAINTOT, B., Granier, T., Huc, Y.

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Funding Organization	Location	Grant Number
Polish Ministry of Science and Higher Education (Mobility Plus Program)	Poland	--

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2017-03-15
  Changes: Database references
• Version 1.2: 2019-06-12
  Changes: Data collection, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 2.1: 2024-01-17
  Changes: Refinement description
• Version 3.0: 2024-09-04
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
• Version 4.0: 2024-12-04
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary