1KY2

GPPNHP-BOUND YPT7P AT 1.6 A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Rab-subfamily-specific regions of Ypt7p are structurally different from other RabGTPases.

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

(2002) Structure 10: 569-579

  • DOI: 10.1016/s0969-2126(02)00737-2
  • Primary Citation of Related Structures:  
    1KY2, 1KY3

  • PubMed Abstract: 

    • The GTPase Ypt7p from S. cerevisiae is involved in late endosome-to-vacuole transport and homotypic vacuole fusion. We present crystal structures of the GDP- and GppNHp-bound conformation of Ypt7p solved at 1.35 and 1.6 A resolution, respectively. Despite the similarity of the overall structure to other Ypt/Rab proteins, Ypt7p displays small but significant differences ...

    The GTPase Ypt7p from S. cerevisiae is involved in late endosome-to-vacuole transport and homotypic vacuole fusion. We present crystal structures of the GDP- and GppNHp-bound conformation of Ypt7p solved at 1.35 and 1.6 A resolution, respectively. Despite the similarity of the overall structure to other Ypt/Rab proteins, Ypt7p displays small but significant differences. The Ypt7p-specific residues Tyr33 and Tyr37 cause a difference in the main chain trace of the RabSF2 region and form a characteristic surface epitope. Ypt7p*GppNHp does not display the helix alpha2, characteristic of the Ras-superfamily, but instead possess an extended loop L4/L5. Due to insertions in loops L3 and L7, the neighboring RabSF1 and RabSF4 regions are different in their conformations to those of other Ypt/Rab proteins.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-BINDING PROTEIN YPT7PA182Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YPT7
UniProt
Find proteins for P32939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32939 
Go to UniProtKB:  P32939
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32939
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.137α = 90
b = 60.667β = 90
c = 73.537γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description