4CA1

Crystal structure of Siah1 at 1.58 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb4CA1/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-04 Released: 2013-10-16 
• Deposition Author(s): Rimsa, V., Eadsforth, T.C., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.189 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

Two High-Resolution Structures of the Human E3 Ubiquitin Ligase Siah1.

Rimsa, V., Eadsforth, T.C., Hunter, W.N.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 96: 1339

• PubMed: 24316825 
• DOI: https://doi.org/10.1107/S1744309113031448
• Primary Citation of Related Structures:  
  4C9Z, 4CA1


• PubMed Abstract: 
  

  Siah1 is an E3 ubiquitin ligase that contributes to proteasome-mediated degradation of multiple targets in key cellular processes and which shows promise as a therapeutic target in oncology. Structures of a truncated Siah1 bound to peptide-based inhibitors have been reported. Here, new crystallization conditions have allowed the determination of a construct encompassing dual zinc-finger subdomains and substrate-binding domains at significantly higher resolution. Although the crystals appear isomorphous, two structures present distinct states in which the spatial orientation of one zinc-finger subdomain differs with respect to the rest of the dimeric protein. Such a difference, which is indicative of conformational freedom, infers potential biological relevance related to recognition of binding partners. The crystallization conditions and improved models of Siah1 may aid future studies investigating Siah1-ligand complexes.

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Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.

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: 45.8 kDa 
• Atom Count: 3,715 
• Modelled Residue Count: 379 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE SIAH1	A, B	195	Homo sapiens	Mutation(s): 0  EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUQ4 (Homo sapiens) Explore Q8IUQ4  Go to UniProtKB:  Q8IUQ4
PHAROS:  Q8IUQ4 GTEx:  ENSG00000196470

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], P [auth B], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H [auth A], O [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.189 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.06	α = 90
b = 104.12	β = 90
c = 133.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Rimsa, V., Eadsforth, T.C., Hunter, W.N.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2013-12-18
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description