Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 224.41 kDa 
• Atom Count: 14637 
• Residue Count: 1837 
• Unique protein chains: 3

6QUY

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

• DOI: 10.2210/pdb6QUY/pdb
• EMDataResource: EMD-4644

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Naegleria gruberi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-28 Released: 2019-11-27 
• Deposition Author(s): Atherton, J.M., Luo, Y., Xiang, S., Yang, C., Jiang, K., Stangier, M., Vemu, A., Cook, A., Wang, S., Roll-Mecak, A., Steinmetz, M.O., Akhmanova, A., Baldus, M., Moores, C.A.
• Funding Organization(s): Medical Research Council (United Kingdom), Swiss National Science Foundation

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Experimental Data Snapshot

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

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

• PubMed: 31748546 
• 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. 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.

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Organizational Affiliation: 

Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Homo sapiens	Mutation(s): 0  Gene Names: TUBA1B
Find proteins for P68363 (Homo sapiens) Explore P68363  Go to UniProtKB:  P68363
NIH Common Fund Data Resources
PHAROS:  P68363 GTEx:  ENSG00000123416

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CKK domain protein	W	187	Naegleria gruberi	Mutation(s): 0  Gene Names: NAEGRDRAFT_50049
Find proteins for D2VJG4 (Naegleria gruberi) Explore D2VJG4  Go to UniProtKB:  D2VJG4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	G, H	444	Homo sapiens	Mutation(s): 0  Gene Names: TUBB, TUBB5, OK/SW-cl.56
Find proteins for P07437 (Homo sapiens) Explore P07437  Go to UniProtKB:  P07437
NIH Common Fund Data Resources
PHAROS:  P07437 GTEx:  ENSG00000196230

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TA1	G, H	TAXOL C47 H51 N O14 RCINICONZNJXQF-MZXODVADSA-N
GTP	A, C	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	G, H	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	A, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-02-28 
• Released Date: 2019-11-27 
Deposition Author(s): Atherton, J.M., Luo, Y., Xiang, S., Yang, C., Jiang, K., Stangier, M., Vemu, A., Cook, A., Wang, S., Roll-Mecak, A., Steinmetz, M.O., Akhmanova, A., Baldus, M., Moores, C.A.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/R000352/1
	Netherlands	722.016.002
	Netherlands	175.010.2009.002
	Netherlands	718.015.001
	Netherlands	184.032.207
Swiss National Science Foundation	Switzerland	31003A_166608

Revision History 

• 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