1EK0

GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.228 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GNPClick on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis.

Esters, H.Alexandrov, K.Constantinescu, A.T.Goody, R.S.Scheidig, A.J.

(2000) J Mol Biol 298: 111-121

  • DOI: https://doi.org/10.1006/jmbi.2000.3645
  • Primary Citation of Related Structures:  
    1EK0

  • PubMed Abstract: 

    Ypt/Rab proteins are membrane-associated small GTP-binding proteins which play a central role in the coordination, activation and regulation of vesicle-mediated transport in eukaryotic cells. We present the 1.5 A high-resolution crystal structure of Ypt51 in its active, GppNHp-bound conformation. Ypt51 is an important regulator involved in the endocytic membrane traffic of Saccharomyces cerevisiae. The structure reveals small but significant structural differences compared with H-Ras p21. The effector loop and the catalytic loop are well defined and stabilized by extensive hydrophobic interactions. The switch I and switch II regions form a well-defined epitope for hypothetical effector protein binding. Sequence comparisons between the different isoforms Ypt51, Ypt52 and Ypt53 provide the first insights into determinants for specific effector binding and for fine-tuning of the intrinsic GTP-hydrolysis rate.


  • Organizational Affiliation

    Abteilung für Physikalische Biochemie, Max-Planck Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (GTP-BINDING PROTEIN YPT51)170Saccharomyces cerevisiaeMutation(s): 2 
UniProt
Find proteins for P36017 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36017 
Go to UniProtKB:  P36017
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36017
Sequence Annotations
Expand
  • Reference Sequence
1EK0_1
020406080100120140160
1EK0_1
VTSIKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLAPMYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKIPLK
UNIPROT P36017
VTSIKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLAPMYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKIPLK
MUTATION
MODIFIED MONOMER
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MHO
Query on MHO
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free:  0.228 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.326α = 90
b = 62.326β = 90
c = 91.221γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GNPClick on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary