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 
  • R-Value Observed: 0.192 

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:  
    5YBV, 5YBU, 5YBJ

  • 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 member 21A (KIF21A) to the cell cortex to control microtubule growth via its C-terminal ankyrin domain ...

    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

    the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KN motif and ankyrin repeat domain-containing protein 2A258Homo sapiensMutation(s): 0 
Gene Names: KANK2ANKRD25KIAA1518MXRA3SIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q63ZY3 (Homo sapiens)
Explore Q63ZY3 
Go to UniProtKB:  Q63ZY3
PHAROS:  Q63ZY3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
KN motif and ankyrin repeat domain-containing protein 2B261Homo sapiensMutation(s): 0 
Gene Names: KANK2ANKRD25KIAA1518MXRA3SIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q63ZY3 (Homo sapiens)
Explore Q63ZY3 
Go to UniProtKB:  Q63ZY3
PHAROS:  Q63ZY3
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF21AC, D22Homo sapiensMutation(s): 0 
Gene Names: KIF21AKIAA1708KIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4S6 (Homo sapiens)
Explore Q7Z4S6 
Go to UniProtKB:  Q7Z4S6
PHAROS:  Q7Z4S6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • 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
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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