3LJU | pdb_00003lju

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.231 (Depositor), 0.235 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1009008107
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 GTEx: ENSG00000105963
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75689
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IP9 Query on IP9 Download:Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X]	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		Interactions Focus chain C [auth X] Focus chain D [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.231 (Depositor), 0.235 (DCC)
R-Value Work: 0.191 (Depositor), 0.198 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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