6CME

Structure of wild-type ISL2-LID in complex with LHX4-LIM1+2

• PDB DOI: https://doi.org/10.2210/pdb6CME/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-04 Released: 2019-04-10 
• Deposition Author(s): Stokes, P.H., Silva, A., Guss, J.M., Matthews, J.M.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Mutation in a flexible linker modulates binding affinity for modular complexes.

Stokes, P.H., Robertson, N.O., Silva, A.P.G., Estephan, T., Trewhella, J., Guss, J.M., Matthews, J.M.

(2019) Proteins 87: 425-429

• PubMed: 30788856 
• DOI: https://doi.org/10.1002/prot.25675
• Primary Citation of Related Structures:  
  6CME


• PubMed Abstract: 
  

  Tandem beta zippers are modular complexes formed between repeated linear motifs and tandemly arrayed domains of partner proteins in which β-strands form upon binding. Studies of such complexes, formed by LIM domain proteins and linear motifs in their intrinsically disordered partners, revealed spacer regions between the linear motifs that are relatively flexible but may affect the overall orientation of the binding modules. We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4-ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker.

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Organizational Affiliation: 

School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 38.02 kDa 
• Atom Count: 2,672 
• Modelled Residue Count: 308 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2	A, B	169	Mus musculus	Mutation(s): 0  Gene Names: Lhx4, Gsh-4, Gsh4, Isl2
UniProt
Find proteins for Q9CXV0 (Mus musculus) Explore Q9CXV0  Go to UniProtKB:  Q9CXV0
Find proteins for P53776 (Mus musculus) Explore P53776  Go to UniProtKB:  P53776
UniProt Groups	Q9CXV0P53776

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.488	α = 90
b = 88.843	β = 111.33
c = 50.303	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Stokes, P.H., Silva, A., Guss, J.M., Matthews, J.M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP140102318

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description