5LDD

Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.496 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Architecture and mechanism of the late endosomal Rab7-like Ypt7 guanine nucleotide exchange factor complex Mon1-Ccz1.

Kiontke, S.Langemeyer, L.Kuhlee, A.Schuback, S.Raunser, S.Ungermann, C.Kummel, D.

(2017) Nat Commun 8: 14034-14034

  • DOI: 10.1038/ncomms14034

  • PubMed Abstract: 
  • The Mon1-Ccz1 complex (MC1) is the guanine nucleotide exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 and is required for endosomal maturation and fusion at the vacuole/lysosome. Here we present the overall architecture of MC1 from Chaetomium ther ...

    The Mon1-Ccz1 complex (MC1) is the guanine nucleotide exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 and is required for endosomal maturation and fusion at the vacuole/lysosome. Here we present the overall architecture of MC1 from Chaetomium thermophilum, and in combining biochemical studies and mutational analysis in yeast, we identify the domains required for catalytic activity, complex assembly and localization of MC1. The crystal structure of a catalytic MC1 core complex bound to Ypt7 provides mechanistic insight into its function. We pinpoint the determinants that allow for a discrimination of the Rab7-like Ypt7 over the Rab5-like Vps21, which are both located on the same membrane. MC1 shares structural similarities with the TRAPP complex, but employs a novel mechanism to promote nucleotide exchange that utilizes a conserved lysine residue of Ypt7, which is inserted upon MC1 binding into the nucleotide-binding pocket of Ypt7 and contributes to specificity.


    Organizational Affiliation

    Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mon1
A, D
166Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SGS3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SGS3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ccz1
B, E
250Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SD94 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SD94
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Rab small monomeric GTPase-like protein
C, F
207Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 1 
Find proteins for G0SGE1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SGE1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.496 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.083α = 90.00
b = 103.812β = 90.00
c = 206.667γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyKU2531/2-1
German Research FoundationGermanySFB944P17

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Author supporting evidence, Data collection