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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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

    Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA [auth C]451Bos taurusMutation(s): 0 
Find proteins for P81947 (Bos taurus)
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Go to UniProtKB:  P81947
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-2B chainB [auth D]445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
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Go to UniProtKB:  Q6B856
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Designed ankyrin repeat proteinC [auth E]169synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide from Centromere protein JD [auth F]23Homo sapiensMutation(s): 0 
Gene Names: CENPJCPAPLAPLIP1
Find proteins for Q9HC77 (Homo sapiens)
Explore Q9HC77 
Go to UniProtKB:  Q9HC77
NIH Common Fund Data Resources
PHAROS:  Q9HC77
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
E [auth C], G [auth D]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth C], H [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

  • Deposited Date: 2015-10-29 
  • Released Date: 2016-10-26 
  • Deposition Author(s): Li, H., Zheng, X.

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