5KMG

Near-atomic cryo-EM structure of PRC1 bound to the microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Near-atomic cryo-EM structure of PRC1 bound to the microtubule.

Kellogg, E.H.Howes, S.Ti, S.C.Ramirez-Aportela, E.Kapoor, T.M.Chacon, P.Nogales, E.

(2016) Proc.Natl.Acad.Sci.USA 113: 9430-9439

  • DOI: 10.1073/pnas.1609903113

  • PubMed Abstract: 
  • Proteins that associate with microtubules (MTs) are crucial to generate MT arrays and establish different cellular architectures. One example is PRC1 (protein regulator of cytokinesis 1), which cross-links antiparallel MTs and is essential for the co ...

    Proteins that associate with microtubules (MTs) are crucial to generate MT arrays and establish different cellular architectures. One example is PRC1 (protein regulator of cytokinesis 1), which cross-links antiparallel MTs and is essential for the completion of mitosis and cytokinesis. Here we describe a 4-Å-resolution cryo-EM structure of monomeric PRC1 bound to MTs. Residues in the spectrin domain of PRC1 contacting the MT are highly conserved and interact with the same pocket recognized by kinesin. We additionally found that PRC1 promotes MT assembly even in the presence of the MT stabilizer taxol. Interestingly, the angle of the spectrin domain on the MT surface corresponds to the previously observed cross-bridge angle between MTs cross-linked by full-length, dimeric PRC1. This finding, together with molecular dynamic simulations describing the intrinsic flexibility of PRC1, suggests that the MT-spectrin domain interface determines the geometry of the MT arrays cross-linked by PRC1.


    Organizational Affiliation

    Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A
441Sus scrofaGene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Go to Gene View: TUBA1B
Go to UniProtKB:  Q2XVP4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B
431Sus scrofa
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein regulator of cytokinesis 1
P
128Homo sapiensGene Names: PRC1
Find proteins for O43663 (Homo sapiens)
Go to Gene View: PRC1
Go to UniProtKB:  O43663
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
POU
Query on POU

Download SDF File 
Download CCD File 
B
Peloruside A
(1R,3R,4S,7S,9S,11S,13R,14R,15R)-4,11,13,14-tetrahydroxy-7-[(2Z,4R)-4-(hydroxymethyl)hex-2-en-2-yl]-3,9,15-trimethoxy-12,12-dimethyl-6,17-dioxabicyclo[11.3.1]heptadecan-5-one
C27 H48 O11
NETARJWZTMGMRM-QOXVJYTGSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM051487
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM65933
Ministerio de Economia y CompetitividadSpainBFU2013-44306-P

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references
  • Version 1.2: 2016-09-07
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Data collection