3FM8 | pdb_00003fm8

Crystal structure of full length centaurin alpha-1 bound with the FHA domain of KIF13B (CAPRI target)

PDB DOI: https://doi.org/10.2210/pdb3FM8/pdb

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

Deposited: 2008-12-19 Released: 2009-08-25
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: 2.30 Å
R-Value Free:
0.272 (Depositor), 0.271 (DCC)
R-Value Work:
0.231 (Depositor), 0.233 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

This is version 1.5 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: 119.75 kDa
Atom Count: 7,335
Modeled Residue Count: 910
Deposited Residue Count: 1,032
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF13B	A, B	124	Homo sapiens	Mutation(s): 0 Gene Names: KIF13B, GAKIN, KIAA0639
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQT8 (Homo sapiens) Explore Q9NQT8 Go to UniProtKB: Q9NQT8
PHAROS: Q9NQT8 GTEx: ENSG00000197892
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NQT8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centaurin-alpha-1	C, D	392	Homo sapiens	Mutation(s): 0 Gene Names: 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain J [auth C] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain J [auth C] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain J [auth C]	J [auth C], R [auth D], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain J [auth C] Focus chain R [auth D] Focus chain S [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain I [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth C]	I [auth C], Q [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain Q [auth D] Interactions & Density Focus chain I [auth C] Focus chain Q [auth D]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain E [auth A] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] E [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], G [auth A], H [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.272 (Depositor), 0.271 (DCC)
R-Value Work: 0.231 (Depositor), 0.233 (DCC)
R-Value Observed: 0.232 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.632	α = 90
b = 115.632	β = 90
c = 189.291	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-09-25
Changes: Derived calculations
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-04-03
Changes: Refinement description