5YBV

The structure of the KANK2 ankyrin domain with the KIF21A peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the recognition of kinesin family member 21A (KIF21A) by the ankyrin domains of KANK1 and KANK2 proteins.

Guo, Q.Liao, S.Zhu, Z.Li, Y.Li, F.Xu, C.

(2018) J. Biol. Chem. 293: 557-566

  • DOI: 10.1074/jbc.M117.817494
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A well-controlled microtubule organization is essential for intracellular transport, cytoskeleton maintenance, and cell development. KN motif and ankyrin repeat domain-containing protein 1 (KANK1), a member of KANK family, recruits kinesin family mem ...

    A well-controlled microtubule organization is essential for intracellular transport, cytoskeleton maintenance, and cell development. KN motif and ankyrin repeat domain-containing protein 1 (KANK1), a member of KANK family, recruits kinesin family member 21A (KIF21A) to the cell cortex to control microtubule growth via its C-terminal ankyrin domain. However, how the KANK1 ankyrin domain recognizes KIF21A and whether other KANK proteins can also bind KIF21A remain unknown. Here, using a combination of structural, site-directed mutagenesis, and biochemical studies, we found that a stretch of ∼22 amino acids in KIF21A is sufficient for binding to KANK1 and its close homolog KANK2. We further solved the complex structure of the KIF21A peptide with either the KANK1 ankyrin domain or the KANK2 ankyrin domain. In each complex, KIF21A is recognized by two distinct pockets of the ankyrin domain and adopts helical conformations upon binding to the ankyrin domain. The elucidated KANK structures may advance our understanding of the role of KANK1 as a scaffolding molecule in controlling microtubule growth at the cell periphery.


    Organizational Affiliation

    From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KN motif and ankyrin repeat domain-containing protein 2
A
258Homo sapiensMutation(s): 0 
Gene Names: KANK2 (ANKRD25, KIAA1518, MXRA3, SIP)
Find proteins for Q63ZY3 (Homo sapiens)
Go to Gene View: KANK2
Go to UniProtKB:  Q63ZY3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
KN motif and ankyrin repeat domain-containing protein 2
B
261Homo sapiensMutation(s): 0 
Gene Names: KANK2 (ANKRD25, KIAA1518, MXRA3, SIP)
Find proteins for Q63ZY3 (Homo sapiens)
Go to Gene View: KANK2
Go to UniProtKB:  Q63ZY3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Kinesin-like protein KIF21A
C, D
22Homo sapiensMutation(s): 0 
Gene Names: KIF21A (KIAA1708, KIF2)
Find proteins for Q7Z4S6 (Homo sapiens)
Go to Gene View: KIF21A
Go to UniProtKB:  Q7Z4S6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.956α = 73.02
b = 52.834β = 89.67
c = 53.478γ = 84.91
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data processing
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references