1KY3

GDP-BOUND YPT7P AT 1.35 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1KY3/pdb

• Classification: ENDOCYTOSIS/EXOCYTOSIS
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 1.35 Å
• R-Value Free: 
  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.63 kDa 
• Atom Count: 1,472 
• Modelled Residue Count: 162 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-BINDING PROTEIN YPT7P	A	182	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ypt7
UniProt
Find proteins for P32939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32939  Go to UniProtKB:  P32939

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.535	α = 90
b = 55.43	β = 90
c = 60.177	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2024-02-14
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description