2P4N | pdb_00002p4n

Human Monomeric Kinesin (1BG2) and Bovine Tubulin (1JFF) Docked into the 9-Angstrom Cryo-EM Map of Nucleotide-Free Kinesin Complexed to the Microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2P4N

This is version 1.3 of the entry. See complete history

Literature

The beginning of kinesin's force-generating cycle visualized at 9-A resolution.

Sindelar, C.V.Downing, K.H.

(2007) J Cell Biol 177: 377-385

  • DOI: https://doi.org/10.1083/jcb.200612090
  • Primary Citation Related Structures: 
    2P4N

  • PubMed Abstract: 

    We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, in kinesin's poorly understood nucleotide-free state. Both of the switch elements undergo conformational change relative to the microtubule-free state. The changes in switch I suggest a role for it in "ejecting" adenosine diphosphate when kinesin initially binds to the microtubule. The switch II helix has an N-terminal extension, apparently stabilized by conserved microtubule contacts, implying a microtubule activation mechanism that could convey the state of the bound nucleotide to kinesin's putative force-delivering element (the "neck linker"). In deriving this structure, we have adapted an image-processing technique, single-particle reconstruction, for analyzing decorated microtubules. The resulting reconstruction visualizes the asymmetric seam present in native, 13-protofilament microtubules, and this method will provide an avenue to higher-resolution characterization of a variety of microtubule- binding proteins, as well as the microtubule itself.


  • Organizational Affiliation
    • Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 138.8 kDa 
  • Atom Count: 9,264 
  • Modeled Residue Count: 1,161 
  • Deposited Residue Count: 1,221 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin heavy chainA [auth K]325Homo sapiensMutation(s): 0 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha chainB [auth A]451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
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UniProt GroupP02550
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chainC [auth B]445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1

Query on TA1



Download:Ideal Coordinates CCD File
J [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP

Query on GTP



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

Query on GDP



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

Query on ADP



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

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth K],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description