4HNA | pdb_00004hna

Kinesin motor domain in the ADP-MG-ALFX state in complex with tubulin and a DARPIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.211 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of a kinesin-tubulin complex and implications for kinesin motility.

Gigant, B.Wang, W.Dreier, B.Jiang, Q.Pecqueur, L.Pluckthun, A.Wang, C.Knossow, M.

(2013) Nat Struct Mol Biol 20: 1001-1007

  • DOI: https://doi.org/10.1038/nsmb.2624
  • Primary Citation Related Structures: 
    4HNA

  • PubMed Abstract: 

    The typical function of kinesins is to transport cargo along microtubules. Binding of ATP to microtubule-attached motile kinesins leads to cargo displacement. To better understand the nature of the conformational changes that lead to the power stroke that moves a kinesin's load along a microtubule, we determined the X-ray structure of human kinesin-1 bound to αβ-tubulin. The structure defines the mechanism of microtubule-stimulated ATP hydrolysis, which releases the kinesin motor domain from microtubules. It also reveals the structural linkages that connect the ATP nucleotide to the kinesin neck linker, a 15-amino acid segment C terminal to the catalytic core of the motor domain, to result in the power stroke. ATP binding to the microtubule-bound kinesin favors neck-linker docking. This biases the attachment of kinesin's second head in the direction of the movement, thus initiating each of the steps taken.


  • Organizational Affiliation
    • Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, Gif sur Yvette, France.

Macromolecule Content 

  • Total Structure Weight: 159.18 kDa 
  • Atom Count: 10,607 
  • Modeled Residue Count: 1,353 
  • Deposited Residue Count: 1,414 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha chain451Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWZ0 (Ovis aries)
Explore D0VWZ0 
Go to UniProtKB:  D0VWZ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWZ0
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain445Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Entity Groups
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UniProt GroupD0VWY9
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2C [auth D]169synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-1 heavy chainD [auth K]349Homo sapiensMutation(s): 0 
Gene Names: KIF5BKNSKNS1
UniProt & NIH Common Fund Data Resources
Find proteins for P33176 (Homo sapiens)
Explore P33176 
Go to UniProtKB:  P33176
PHAROS:  P33176
GTEx:  ENSG00000170759 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33176
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
G [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
J [auth K]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF

Query on ALF



Download:Ideal Coordinates CCD File
I [auth B],
L [auth K]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.211 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.05α = 90
b = 160.54β = 90
c = 174.95γ = 90
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
SAWAYAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Source and taxonomy
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description