5EIB

Crystal structure of CPAP PN2-3 C-terminal loop-helix in complex with DARPin-tubulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular basis for CPAP-tubulin interaction in controlling centriolar and ciliary length

Zheng, X.Ramani, A.Soni, K.Gottardo, M.Zheng, S.Ming Gooi, L.Li, W.Feng, S.Mariappan, A.Wason, A.Widlund, P.Pozniakovsky, A.Poser, I.Deng, H.Ou, G.Riparbelli, M.Giuliano, C.Hyman, A.A.Sattler, M.Gopalakrishnan, J.Li, H.

(2016) Nat Commun 7: 11874-11874

  • DOI: https://doi.org/10.1038/ncomms11874
  • Primary Citation of Related Structures:  
    5EIB

  • PubMed Abstract: 

    Centrioles and cilia are microtubule-based structures, whose precise formation requires controlled cytoplasmic tubulin incorporation. How cytoplasmic tubulin is recognized for centriolar/ciliary-microtubule construction remains poorly understood. Centrosomal-P4.1-associated-protein (CPAP) binds tubulin via its PN2-3 domain. Here, we show that a C-terminal loop-helix in PN2-3 targets β-tubulin at the microtubule outer surface, while an N-terminal helical motif caps microtubule's α-β surface of β-tubulin. Through this, PN2-3 forms a high-affinity complex with GTP-tubulin, crucial for defining numbers and lengths of centriolar/ciliary-microtubules. Surprisingly, two distinct mutations in PN2-3 exhibit opposite effects on centriolar/ciliary-microtubule lengths. CPAP(F375A), with strongly reduced tubulin interaction, causes shorter centrioles and cilia exhibiting doublet- instead of triplet-microtubules. CPAP(EE343RR) that unmasks the β-tubulin polymerization surface displays slightly reduced tubulin-binding affinity inducing over-elongation of newly forming centriolar/ciliary-microtubules by enhanced dynamic release of its bound tubulin. Thus CPAP regulates delivery of its bound-tubulin to define the size of microtubule-based cellular structures using a 'clutch-like' mechanism.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA [auth C]451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
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UniProt GroupP81947
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chainB [auth D]445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
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UniProt GroupQ6B856
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Designed ankyrin repeat proteinC [auth E]169synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Centromere protein JD [auth F]23Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC77 (Homo sapiens)
Explore Q9HC77 
Go to UniProtKB:  Q9HC77
PHAROS:  Q9HC77
GTEx:  ENSG00000151849 
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UniProt GroupQ9HC77
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.856α = 90
b = 91.116β = 96.97
c = 83.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description