6EI6 | pdb_00006ei6

CC2D1B coordinates ESRCT-III activity during the mitotic reformation of the nuclear envelope

PDB DOI: https://doi.org/10.2210/pdb6EI6/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2017-09-18 Released: 2018-10-10
Deposition Author(s): Ventimiglia, L.N., Cuesta-Geijo, M.A., Martinelli, N., Caballe, A., Macheboeuf, P., Miguet, N., Parnham, I.M., Olmos, Y., Carlton, J.G., Weissehorn, W., martin-Serrano, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.205 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

CC2D1B Coordinates ESCRT-III Activity during the Mitotic Reformation of the Nuclear Envelope.

Ventimiglia, L.N., Cuesta-Geijo, M.A., Martinelli, N., Caballe, A., Macheboeuf, P., Miguet, N., Parnham, I.M., Olmos, Y., Carlton, J.G., Weissenhorn, W., Martin-Serrano, J.

(2018) Dev Cell 47: 547-563.e6

PubMed: 30513301 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.devcel.2018.11.012
Primary Citation Related Structures:
6EI6

PubMed Abstract:
The coordinated reformation of the nuclear envelope (NE) after mitosis re-establishes the structural integrity and the functionality of the nuclear compartment. The endosomal sorting complex required for transport (ESCRT) machinery, a membrane remodeling pathway that is highly conserved in eukaryotes, has been recently involved in NE resealing by mediating the annular fusion of the nuclear membrane (NM). We show here that CC2D1B, a regulator of ESCRT polymerization, is required to re-establish the nuclear compartmentalization by coordinating endoplasmic reticulum (ER) membrane deposition around chromatin disks with ESCRT-III recruitment to the reforming NE. Accordingly, CC2D1B determines the spatiotemporal distribution of the CHMP7-ESCRT-III axis during NE reformation. Crucially, in CC2D1B-depleted cells, ESCRT activity is uncoupled from Spastin-mediated severing of spindle microtubules, resulting in persisting microtubules that compromise nuclear morphology. Therefore, we reveal CC2D1B as an essential regulatory factor that licenses the formation of ESCRT-III polymers to ensure the orderly reformation of the NE.

Organizational Affiliation

Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London SE1 9RT, UK.

Macromolecule Content

Total Structure Weight: 63.26 kDa
Atom Count: 4,169
Modeled Residue Count: 484
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coiled-coil and C2 domain-containing protein 1-like	A, B	270	Drosophila melanogaster	Mutation(s): 0 Gene Names: l(2)gd1, lgd, CG4713 Membrane Entity: Yes
UniProt
Find proteins for Q9VKJ9 (Drosophila melanogaster) Explore Q9VKJ9 Go to UniProtKB: Q9VKJ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VKJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.247 (Depositor), 0.247 (DCC)
R-Value Work: 0.205 (Depositor), 0.207 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.41	α = 90
b = 54.05	β = 99.52
c = 97.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
Auto-Rickshaw	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2018-12-19
Changes: Data collection, Database references, Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Structure summary