8C5C | pdb_00008c5c

microtubule decorated with tubulin oligomers in presence of APC C-terminal domain. (here only map corresponding to the 13-pf microtubule is represented)

  • Classification: CELL CYCLE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2023-01-06 Released: 2023-01-25 
  • Deposition Author(s): Serre, L., Arnal, I.
  • Funding Organization(s): ATIP-Avenir

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 8C5C

This is version 1.2 of the entry. See complete history

Literature

The mitotic role of adenomatous polyposis coli requires its bilateral interaction with tubulin and microtubules.

Serre, L.Delaroche, J.Vinit, A.Schoehn, G.Denarier, E.Fourest-Lieuvin, A.Arnal, I.

(2023) J Cell Sci 136

  • DOI: https://doi.org/10.1242/jcs.260152
  • Primary Citation Related Structures: 
    8C5C

  • PubMed Abstract: 

    Adenomatous polyposis coli (APC) is a scaffold protein with tumour suppressor properties. Mutations causing the loss of its C-terminal domain (APC-C), which bears cytoskeleton-regulating sequences, correlate with colorectal cancer. The cellular roles of APC in mitosis are widely studied, but the molecular mechanisms of its interaction with the cytoskeleton are poorly understood. Here, we investigated how APC-C regulates microtubule properties, and found that it promotes both microtubule growth and shrinkage. Strikingly, APC-C accumulates at shrinking microtubule extremities, a common characteristic of depolymerases. Cryo-electron microscopy revealed that APC-C adopts an extended conformation along the protofilament crest and showed the presence of ring-like tubulin oligomers around the microtubule wall, which required the presence of two APC-C sub-domains. A mutant of APC-C that was incapable of decorating microtubules with ring-like tubulin oligomers exhibited a reduced effect on microtubule dynamics. Finally, whereas native APC-C rescued defective chromosome alignment in metaphase cells silenced for APC, the ring-incompetent mutant failed to correct mitotic defects. Thus, the bilateral interaction of APC-C with tubulin and microtubules likely contributes to its mitotic functions.


  • Organizational Affiliation
    • Université Grenoble Alpes, Inserm U1216, CEA, CNRS, Grenoble Institut Neurosciences, GIN, 38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 2,629.81 kDa 
  • Atom Count: 178,971 
  • Modeled Residue Count: 22,620 
  • Deposited Residue Count: 23,322 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain446Bos taurusMutation(s): 0 
UniProt
Find proteins for A0A452DIL8 (Bos taurus)
Explore A0A452DIL8 
Go to UniProtKB:  A0A452DIL8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A452DIL8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
(Subject of Investigation/LOI)

Query on TA1



Download:Ideal Coordinates CCD File
AB [auth a]
CB [auth b]
EB [auth c]
GB [auth d]
IB [auth e]
AB [auth a],
CB [auth b],
EB [auth c],
GB [auth d],
IB [auth e],
KB [auth f],
MB [auth g],
OB [auth h],
QB [auth i],
SB [auth j],
UB [auth k],
WB [auth l],
YB [auth m]
TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP
(Subject of Investigation/LOI)

Query on GTP



Download:Ideal Coordinates CCD File
BC [auth N]
DC [auth O]
FC [auth P]
HC [auth Q]
JC [auth R]
BC [auth N],
DC [auth O],
FC [auth P],
HC [auth Q],
JC [auth R],
LC [auth S],
NC [auth T],
PC [auth U],
RC [auth V],
TC [auth W],
VC [auth X],
XC [auth Y],
ZC [auth Z]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
BB [auth a]
DB [auth b]
FB [auth c]
HB [auth d]
JB [auth e]
BB [auth a],
DB [auth b],
FB [auth c],
HB [auth d],
JB [auth e],
LB [auth f],
NB [auth g],
PB [auth h],
RB [auth i],
TB [auth j],
VB [auth k],
XB [auth l],
ZB [auth m]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AC [auth N]
CC [auth O]
EC [auth P]
GC [auth Q]
IC [auth R]
AC [auth N],
CC [auth O],
EC [auth P],
GC [auth Q],
IC [auth R],
KC [auth S],
MC [auth T],
OC [auth U],
QC [auth V],
SC [auth W],
UC [auth X],
WC [auth Y],
YC [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ATIP-AvenirFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary