5LDD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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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: https://doi.org/10.1038/ncomms14034
  • Primary Citation of Related Structures:  
    5LDD

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mon1
A, D
166Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0067370
UniProt
Find proteins for G0SGS3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SGS3 
Go to UniProtKB:  G0SGS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SGS3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ccz1
B, E
250Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0050970
UniProt
Find proteins for G0SD94 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SD94 
Go to UniProtKB:  G0SD94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SD94
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rab small monomeric GTPase-like protein
C, F
207Thermochaetoides thermophila DSM 1495Mutation(s): 1 
Gene Names: CTHT_0065990
UniProt
Find proteins for G0SGE1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SGE1 
Go to UniProtKB:  G0SGE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SGE1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.083α = 90
b = 103.812β = 90
c = 206.667γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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