6QUY

NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural determinants of microtubule minus end preference in CAMSAP CKK domains.

Atherton, J., Luo, Y., Xiang, S., Yang, C., Rai, A., Jiang, K., Stangier, M., Vemu, A., Cook, A.D., Wang, S., Roll-Mecak, A., Steinmetz, M.O., Akhmanova, A., Baldus, M., Moores, C.A.

(2019) Nat Commun 10: 5236-5236

  • DOI: 10.1038/s41467-019-13247-6
  • Primary Citation of Related Structures:  
    6QUS, 6QUY, 6QVE, 6QVJ

  • PubMed Abstract: 

    • CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which lacks minus-end specificity ...

    CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which lacks minus-end specificity. Here we report near-atomic cryo-electron microscopy structures of HsCKK- and NgCKK-microtubule complexes, which show that these CKK domains share the same protein fold, bind at the intradimer interprotofilament tubulin junction, but exhibit different footprints on microtubules. NMR experiments show that both HsCKK and NgCKK are remarkably rigid. However, whereas NgCKK binding does not alter the microtubule architecture, HsCKK remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. Thus, in contrast to many MAPs, the HsCKK domain can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition.

    Organizational Affiliation: 

    Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, UK. c.moores@mail.cryst.bbk.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA,
B [auth C]		451Homo sapiensMutation(s): 0 
Gene Names: TUBA1B
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens)
Explore P68363 
Go to UniProtKB:  P68363
PHAROS:  P68363
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UniProt GroupP68363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CKK domain proteinC [auth W]187Naegleria gruberiMutation(s): 0 
Gene Names: NAEGRDRAFT_50049
UniProt
Find proteins for D2VJG4 (Naegleria gruberi)
Explore D2VJG4 
Go to UniProtKB:  D2VJG4
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UniProt GroupD2VJG4
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainE [auth G],
D [auth H]		444Homo sapiensMutation(s): 0 
Gene Names: TUBB, TUBB5, OK/SW-cl.56
UniProt & NIH Common Fund Data Resources
Find proteins for P07437 (Homo sapiens)
Explore P07437 
Go to UniProtKB:  P07437
PHAROS:  P07437
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UniProt GroupP07437
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1
Download Ideal Coordinates CCD File 
K [auth H],
M [auth G]		TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N		 Ligand Interaction
GTP
Query on GTP
Download Ideal Coordinates CCD File 
F [auth A],
H [auth C]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
J [auth H],
L [auth G]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
I [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TA1 BindingDB:  6QUY EC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/R000352/1
Netherlands722.016.002
Netherlands175.010.2009.002
Netherlands718.015.001
Netherlands184.032.207
Swiss National Science FoundationSwitzerland31003A_166608

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2021-02-10
    Changes: Source and taxonomy