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- PDB-8c5c: microtubule decorated with tubulin oligomers in presence of APC C... -

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Basic information

Entry
Database: PDB / ID: 8c5c
Titlemicrotubule decorated with tubulin oligomers in presence of APC C-terminal domain. (here only map corresponding to the 13-pf microtubule is represented)
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / cytoskeleton / microtubule
Function / homology
Function and homology information


cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule ...cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin beta 4B class IVb / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsSerre, L. / Arnal, I.
Funding support France, 1items
OrganizationGrant numberCountry
ATIP-Avenir France
CitationJournal: J Cell Sci / Year: 2023
Title: The mitotic role of adenomatous polyposis coli requires its bilateral interaction with tubulin and microtubules.
Authors: Laurence Serre / Julie Delaroche / Angélique Vinit / Guy Schoehn / Eric Denarier / Anne Fourest-Lieuvin / Isabelle Arnal /
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, ...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.
History
DepositionJan 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Tubulin beta chain
b: Tubulin beta chain
c: Tubulin beta chain
d: Tubulin beta chain
e: Tubulin beta chain
f: Tubulin beta chain
g: Tubulin beta chain
h: Tubulin beta chain
i: Tubulin beta chain
j: Tubulin beta chain
k: Tubulin beta chain
l: Tubulin beta chain
m: Tubulin beta chain
N: Tubulin alpha-1B chain
O: Tubulin alpha-1B chain
P: Tubulin alpha-1B chain
Q: Tubulin alpha-1B chain
R: Tubulin alpha-1B chain
S: Tubulin alpha-1B chain
T: Tubulin alpha-1B chain
U: Tubulin alpha-1B chain
V: Tubulin alpha-1B chain
W: Tubulin alpha-1B chain
X: Tubulin alpha-1B chain
Y: Tubulin alpha-1B chain
Z: Tubulin alpha-1B chain
A: Tubulin alpha-1B chain
B: Tubulin alpha-1B chain
C: Tubulin alpha-1B chain
D: Tubulin alpha-1B chain
E: Tubulin alpha-1B chain
F: Tubulin alpha-1B chain
G: Tubulin alpha-1B chain
H: Tubulin alpha-1B chain
I: Tubulin alpha-1B chain
J: Tubulin alpha-1B chain
K: Tubulin alpha-1B chain
L: Tubulin alpha-1B chain
M: Tubulin alpha-1B chain
n: Tubulin beta chain
o: Tubulin beta chain
p: Tubulin beta chain
q: Tubulin beta chain
r: Tubulin beta chain
s: Tubulin beta chain
t: Tubulin beta chain
u: Tubulin beta chain
v: Tubulin beta chain
w: Tubulin beta chain
x: Tubulin beta chain
y: Tubulin beta chain
z: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,629,813104
Polymers2,605,83452
Non-polymers23,98052
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area206040 Å2
ΔGint-865 kcal/mol
Surface area729190 Å2
MethodPISA

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Components

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Protein , 2 types, 52 molecules abcdefghijklmnopqrstuvwxyzNOPQ...

#1: Protein ...
Tubulin beta chain


Mass: 50019.922 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: brain / References: UniProt: A0A452DIL8
#2: Protein ...
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: brain / References: UniProt: P81947

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Non-polymers , 4 types, 52 molecules

#3: Chemical
ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C47H51NO14 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: microtubule / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 6.75
Buffer component
IDConc.NameFormulaBuffer-ID
180 mMPiPESPiPes1
21 mMEGTAEGTA1
31 mMmagnesium chlorideMgCl21
450 mMpotassieum chlorideKCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 37 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4CTFFINDCTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -27.68 ° / Axial rise/subunit: 9.54 Å / Axial symmetry: C1
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11670 / Details: resolution deduced from unmasked FSC is 7.1 A / Symmetry type: HELICAL

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