Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20706.26 
• Atom Count: 1463 
• Residue Count: 182 
• Unique protein chains: 1

1KY2

GPPNHP-BOUND YPT7P AT 1.6 A RESOLUTION

• DOI: 10.2210/pdb1KY2/pdb

• Classification: ENDOCYTOSIS/EXOCYTOSIS
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2002-02-02 Released: 2002-06-05 
• Deposition Author(s): Constantinescu, A.-T., Rak, A., Scheidig, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.249 
• R-Value Work: 0.183 

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

• PubMed: 11937061 
• Primary Citation of Related Structures:  
  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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GTP-BINDING PROTEIN YPT7P	A	182	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: YPT7 (VAM4)
Find proteins for P32939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P32939

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GNP	A	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.249 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 40.137	α = 90.00
b = 60.667	β = 90.00
c = 73.537	γ = 90.00

Software Package:

Software Name	Purpose
SHELXL-97	refinement
AMoRE	phasing
XDS	data scaling
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-02 
• Released Date: 2002-06-05 
• Deposition Author(s): Constantinescu, A.-T., Rak, A., Scheidig, A.J.

Revision History 

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