3H1U

Structure of ubiquitin in complex with Cd ions

• PDB DOI: https://doi.org/10.2210/pdb3H1U/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2009-04-14 Released: 2009-05-05 
• Deposition Author(s): Qureshi, I.A., Ferron, F., Cheung, P., Lescar, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Crystallographic structure of ubiquitin in complex with cadmium ions

Qureshi, I.A., Ferron, F., Seh, C.C., Cheung, P., Lescar, J.

(2009) BMC Res Notes 2: 251-251

• PubMed: 20003470 
• DOI: https://doi.org/10.1186/1756-0500-2-251
• Primary Citation of Related Structures:  
  3H1U


• PubMed Abstract: 
  

  Ubiquitination plays a critical role in regulating many cellular processes, from DNA repair and gene transcription to cell cycle and apoptosis. It is catalyzed by a specific enzymatic cascade ultimately leading to the conjugation of ubiquitin to lysine residues of the target protein that can be the ubiquitin molecule itself and to the formation of poly-ubiquitin chains.

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Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.

Biological Assembly 1  

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

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

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: 17.72 kDa 
• Atom Count: 1,241 
• Modelled Residue Count: 150 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, B	76	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.231	α = 90
b = 105.231	β = 90
c = 105.231	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Qureshi, I.A., Ferron, F., Cheung, P., Lescar, J.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description