4A5X | pdb_00004a5x

Structures of MITD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.227 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4A5X

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

  • 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: 24.39 kDa 
  • Atom Count: 1,529 
  • Modeled Residue Count: 176 
  • Deposited Residue Count: 204 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MIT DOMAIN-CONTAINING PROTEIN 1
A, B
86Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WV92
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CHARGED MULTIVESICULAR BODY PROTEIN 1A
C, D
16Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD42 (Homo sapiens)
Explore Q9HD42 
Go to UniProtKB:  Q9HD42
PHAROS:  Q9HD42
GTEx:  ENSG00000131165 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HD42
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.227 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.07α = 90
b = 74.16β = 90
c = 89.785γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references, Structure summary
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description