3LJU

Crystal structure of full length centaurin alpha-1 bound with the head group of PIP3

• PDB DOI:  https://doi.org/10.2210/pdb3LJU/pdb

• Classification: HYDROLASE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-26 Released: 2010-11-24 
• Deposition Author(s): Shen, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Phosphorylation-independent dual-site binding of the FHA domain of KIF13 mediates phosphoinositide transport via centaurin alpha1.

Tong, Y., Tempel, W., Wang, H., Yamada, K., Shen, L., Senisterra, G.A., MacKenzie, F., Chishti, A.H., Park, H.W.

(2010) Proc Natl Acad Sci U S A 107: 20346-20351

• PubMed: 21057110 
• DOI: https://doi.org/10.1073/pnas.1009008107
• Primary Citation of Related Structures:  
  3FEH, 3FM8, 3LJU


• PubMed Abstract: 
  

Phosphatidylinositol 3,4,5-triphosphate (PIP3) plays a key role in neuronal polarization and axon formation. PIP3-containing vesicles are transported to axon tips by the kinesin KIF13B via an adaptor protein, centaurin α1 (CENTA1). KIF13B interacts with CENTA1 through its forkhead-associated (FHA) domain. We solved the crystal structures of CENTA1 in ligand-free, KIF13B-FHA domain-bound, and PIP3 head group (IP4)-bound conformations, and the CENTA1/KIF13B-FHA/IP4 ternary complex. The first pleckstrin homology (PH) domain of CENTA1 specifically binds to PIP3, while the second binds to both PIP3 and phosphatidylinositol 3,4-biphosphate (PI(3,4)P(2)). The FHA domain of KIF13B interacts with the PH1 domain of one CENTA1 molecule and the ArfGAP domain of a second CENTA1 molecule in a threonine phosphorylation-independent fashion. We propose that full-length KIF13B and CENTA1 form heterotetramers that can bind four phosphoinositide molecules in the vesicle and transport it along the microtubule.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.72 kDa 
• Atom Count: 3,415 
• Modelled Residue Count: 373 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arf-GAP with dual PH domain-containing protein 1	A [auth X]	386	Homo sapiens	Mutation(s): 0  Gene Names: ADAP1, CENTA1
UniProt & NIH Common Fund Data Resources
Find proteins for O75689 (Homo sapiens) Explore O75689  Go to UniProtKB:  O75689
PHAROS:  O75689

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IP9	C [auth X], D [auth X]	(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate C25 H50 O22 P4 ANFYVAHJWGJYAT-QLCNXWICSA-N
ZN	B [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m33lju

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.727	α = 90
b = 66.414	β = 90
c = 127.219	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Shen, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary