Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 21.35 kDa 
• Atom Count: 1689 
• Modelled Residue Count: 175 
• Deposited Residue Count: 180 
• Unique protein chains: 1

3IIK

The structure of hCINAP-SO4 complex at 1.95 angstroms resolution

• PDB DOI: 10.2210/pdb3IIK/pdb

• Classification: PROTEIN BINDING, TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-02 Released: 2010-10-06 
• Deposition Author(s): Zographos, S.E., Drakou, C.E., Leonidas, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.206 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: Structural and functional studies.

Drakou, C.E., Malekkou, A., Hayes, J.M., Lederer, C.W., Leonidas, D.D., Oikonomakos, N.G., Lamond, A.I., Santama, N., Zographos, S.E.

(2012) Proteins 80: 206-220

• PubMed: 22038794 
• DOI: 10.1002/prot.23186
• Primary Citation of Related Structures:  
  3IIJ, 3IIK, 3IIL, 3IIM


• PubMed Abstract: 
  

Human coilin interacting nuclear ATPase protein (hCINAP) directly interacts with coilin, a marker protein of Cajal Bodies (CBs), nuclear organelles involved in the maturation of small nuclear ribonucleoproteins UsnRNPs and snoRNPs. hCINAP has previously been designated as an adenylate kinase (AK6), but is very atypical as it exhibits unusually broad substrate specificity, structural features characteristic of ATPase/GTPase proteins (Walker motifs A and B) and also intrinsic ATPase activity. Despite its intriguing structure, unique properties and cellular localization, the enzymatic mechanism and biological function of hCINAP have remained poorly characterized. Here, we offer the first high-resolution structure of hCINAP in complex with the substrate ADP (and dADP), the structure of hCINAP with a sulfate ion bound at the AMP binding site, and the structure of the ternary complex hCINAP-Mg(2+) ADP-Pi. Induced fit docking calculations are used to predict the structure of the hCINAP-Mg(2+) ATP-AMP ternary complex. Structural analysis suggested a functional role for His79 in the Walker B motif. Kinetic analysis of mutant hCINAP-H79G indicates that His79 affects both AK and ATPase catalytic efficiency and induces homodimer formation. Finally, we show that in vivo expression of hCINAP-H79G in human cells is toxic and drastically deregulates the number and appearance of CBs in the cell nucleus. Our findings suggest that hCINAP may not simply regulate nucleotide homeostasis, but may have broader functionality, including control of CB assembly and disassembly in the nucleus of human cells.

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Organizational Affiliation: 

Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Athens 11635, Greece.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coilin-interacting nuclear ATPase protein	A	180	Homo sapiens	Mutation(s): 0  Gene Names: CINAP, TAF9, hCG_37060, AK6, AD-004, CGI-137 EC: 2.7.4.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D8 (Homo sapiens) Explore Q9Y3D8  Go to UniProtKB:  Q9Y3D8
PHAROS:  Q9Y3D8 GTEx:  ENSG00000085231

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.206 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.67	α = 90
b = 98.67	β = 90
c = 57.65	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-02 
• Released Date: 2010-10-06 
Deposition Author(s): Zographos, S.E., Drakou, C.E., Leonidas, D.D.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-05
  Changes: Advisory, Database references
• Version 1.3: 2011-11-23
  Changes: Database references
• Version 1.4: 2012-01-18
  Changes: Database references