2YMB | pdb_00002ymb

Structures of MITD1

• PDB DOI: https://doi.org/10.2210/pdb2YMB/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-08 Released: 2012-10-24 
• Deposition Author(s): Hadders, M.A., Agromayor, M., Obita, T., Perisic, O., Caballe, A., Kloc, M., Lamers, M.H., Williams, R.L., Martin-Serrano, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Models: experimental

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 
• 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.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.93 kDa 
• Atom Count: 6,629 
• Modeled Residue Count: 794 
• Deposited Residue Count: 1,056 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MIT DOMAIN-CONTAINING PROTEIN 1	A, B, C, D	257	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CHARGED MULTIVESICULAR BODY PROTEIN 1A	E [auth F], F [auth H]	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD42 (Homo sapiens) Explore Q9HD42  Go to UniProtKB:  Q9HD42
PHAROS:  Q9HD42 GTEx:  ENSG00000131165

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.256 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.046	α = 90
b = 222.046	β = 90
c = 222.046	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Hadders, M.A., Agromayor, M., Obita, T., Perisic, O., Caballe, A., Kloc, M., Lamers, M.H., Williams, R.L., Martin-Serrano, J.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description