5XXX

GMPCPP-microtubule complexed with nucleotide-free KIF5C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.43 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport

Shima, T.Morikawa, M.Kaneshiro, J.Kambara, T.Kamimura, S.Yagi, T.Iwamoto, H.Uemura, S.Shigematsu, H.Shirouzu, M.Ichimura, T.Watanabe, T.M.Nitta, R.Okada, Y.Hirokawa, N.

(2018) J Cell Biol 217: 4164-4183

  • DOI: 10.1083/jcb.201711178
  • Primary Citation of Related Structures:  
    5XXT, 5XXV, 5XXX, 5XXW

  • PubMed Abstract: 
  • Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood ...

    Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule.


    Organizational Affiliation

    Center of Excellence in Genome Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1A chain
A, C, E, G, I, K, M, O
A, C, E, G, I, K, M, O, Q
438Sus scrofaMutation(s): 0 
Gene Names: TUBA1A
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chain
B, D, F, H, J, L, N, P
B, D, F, H, J, L, N, P, R
426Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth E] , EA [auth G] , IA [auth I] , MA [auth K] , QA [auth M] , S [auth A] , UA [auth O] , W [auth C] , 
AA [auth E],  EA [auth G],  IA [auth I],  MA [auth K],  QA [auth M],  S [auth A],  UA [auth O],  W [auth C],  YA [auth Q]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
G2P
Query on G2P

Download Ideal Coordinates CCD File 
AB [auth R] , CA [auth F] , GA [auth H] , KA [auth J] , OA [auth L] , SA [auth N] , U [auth B] , WA [auth P] , 
AB [auth R],  CA [auth F],  GA [auth H],  KA [auth J],  OA [auth L],  SA [auth N],  U [auth B],  WA [auth P],  Y [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E] , BB [auth R] , DA [auth F] , FA [auth G] , HA [auth H] , JA [auth I] , LA [auth J] , NA [auth K] , 
BA [auth E],  BB [auth R],  DA [auth F],  FA [auth G],  HA [auth H],  JA [auth I],  LA [auth J],  NA [auth K],  PA [auth L],  RA [auth M],  T [auth A],  TA [auth N],  V [auth B],  VA [auth O],  X [auth C],  XA [auth P],  Z [auth D],  ZA [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.43 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan23000013
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16H06372
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H05897
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan15K08168

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other