5CMW

Crystal structure of yeast Ent5 N-terminal domain-soaked in KI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional insight into the N-terminal domain of the clathrin adaptor Ent5 from Saccharomyces cerevisiae

Zhang, F.Song, Y.Ebrahimi, M.Niu, L.Teng, M.K.Li, X.

(2016) Biochem Biophys Res Commun 477: 786-793

  • DOI: 10.1016/j.bbrc.2016.06.136
  • Primary Citation of Related Structures:  
    5CMW, 5CMY, 5J08

  • PubMed Abstract: 
  • Clathrin-coated vesicles (CCVs) play critical roles in multiple cellular processes, including nutrient uptake, endosome/lysosome biogenesis, pathogen invasion, regulation of signalling receptors, etc. Saccharomyces cerevisiae Ent5 (ScEnt5) is one of ...

    Clathrin-coated vesicles (CCVs) play critical roles in multiple cellular processes, including nutrient uptake, endosome/lysosome biogenesis, pathogen invasion, regulation of signalling receptors, etc. Saccharomyces cerevisiae Ent5 (ScEnt5) is one of the two major adaptors supporting the CCV-mediated TGN/endosome traffic in yeast cells. However, the classification and phosphoinositide binding characteristic of ScEnt5 remain elusive. Here we report the crystal structures of the ScEnt5 N-terminal domain, and find that ScEnt5 contains an insertion α' helix that does not exist in other ENTH or ANTH domains. Furthermore, we investigate the classification of ScEnt5-N(31-191) by evolutionary history analyses and structure comparisons, and find that the ScEnt5 N-terminal domain shows different phosphoinositide binding property from rEpsin1 and rCALM. Above results facilitate the understanding of the ScEnt5-mediated vesicle coat formation process.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China; Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China. Electronic address: sachem@ustc.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epsin-5A170Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENT5YDR153C
Find proteins for Q03769 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03769 
Go to UniProtKB:  Q03769
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.29α = 90
b = 51.76β = 103.42
c = 59.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Chinese Ministry of Science and TechnologyChina2012CB917200 and 2009CB825500
the Chinese National Natural Science FoundationChina31270014, 31130018, 30900224 and 10979039

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references