4A5Z | pdb_00004a5z

Structures of MITD1

PDB DOI: https://doi.org/10.2210/pdb4A5Z/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2011-10-30 Released: 2012-11-14
Deposition Author(s): Hadders, M.A., Agromayor, M., Caballe, A., Obita, T., Perisic, O., Williams, R.L., Martin-Serrano, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.222 (Depositor), 0.234 (DCC)
R-Value Work:
0.191 (Depositor), 0.196 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Escrt-III Binding Protein Mitd1 is Involved in Cytokinesis and Has an Unanticipated Pld Fold that Binds Membranes.

Hadders, M.A., Agromayor, M., Obita, T., Perisic, O., Caballe, A., Kloc, M., Lamers, M.H., Williams, R.L., Martin-Serrano, J.

(2012) Proc Natl Acad Sci U S A 109: 17424

PubMed: 23045692 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1206839109
Primary Citation Related Structures:
2YMB, 4A5X, 4A5Z

PubMed Abstract:
The endosomal sorting complexes required for transport (ESCRT) proteins have a critical function in abscission, the final separation of the daughter cells during cytokinesis. Here, we describe the structure and function of a previously uncharacterized ESCRT-III interacting protein, MIT-domain containing protein 1 (MITD1). Crystal structures of MITD1 reveal a dimer, with a microtubule-interacting and trafficking (MIT) domain at the N terminus and a unique, unanticipated phospholipase D-like (PLD) domain at the C terminus that binds membranes. We show that the MIT domain binds to a subset of ESCRT-III subunits and that this interaction mediates MITD1 recruitment to the midbody during cytokinesis. Depletion of MITD1 causes a distinct cytokinetic phenotype consistent with destabilization of the midbody and abscission failure. These results suggest a model whereby MITD1 coordinates the activity of ESCRT-III during abscission with earlier events in the final stages of cell division.

Organizational Affiliation

Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, United Kingdom.

Macromolecule Content

Total Structure Weight: 79.26 kDa
Atom Count: 5,479
Modeled Residue Count: 624
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MIT DOMAIN-CONTAINING PROTEIN 1	A, B, C, D	163	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WV92 (Homo sapiens) Explore Q8WV92 Go to UniProtKB: Q8WV92
PHAROS: Q8WV92 GTEx: ENSG00000158411
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WV92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth B] I [auth B] J [auth C] F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.222 (Depositor), 0.234 (DCC)
R-Value Work: 0.191 (Depositor), 0.196 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.02	α = 90
b = 109.41	β = 100.55
c = 74.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-14
Type: Initial release
Version 1.1: 2013-11-13
Changes: Data collection, Database references
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, Structure summary