1UKV | pdb_00001ukv

Structure of RabGDP-dissociation inhibitor in complex with prenylated YPT1 GTPase

PDB DOI: https://doi.org/10.2210/pdb1UKV/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-09-01 Released: 2004-09-01
Deposition Author(s): Rak, A., Pylypenko, O., Durek, T., Watzke, A., Kushnir, S., Brunsveld, L., Waldmann, H., Goody, R.S., Alexandrov, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.216 (Depositor), 0.210 (DCC)
R-Value Work:
0.192 (Depositor), 0.187 (DCC)
R-Value Observed:
0.192 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase

Rak, A., Pylypenko, O., Durek, T., Watzke, A., Kushnir, S., Brunsveld, L., Waldmann, H., Goody, R.S., Alexandrov, K.

(2003) Science 302: 646-650

PubMed: 14576435 Search on PubMed
DOI: https://doi.org/10.1126/science.1087761
Primary Citation Related Structures:
1UKV

PubMed Abstract:
Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.

Organizational Affiliation

Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 75.45 kDa
Atom Count: 6,126
Modeled Residue Count: 639
Deposited Residue Count: 659
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secretory pathway GDP dissociation inhibitor	A [auth G]	453	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P39958 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39958 Go to UniProtKB: P39958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39958
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein YPT1	B [auth Y]	206	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P01123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P01123 Go to UniProtKB: P01123
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01123
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain E [auth Y] MOL2 format, chain E [auth Y] mmCIF format, chain E [auth Y]	E [auth Y]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth Y] Interactions & Density Focus chain E [auth Y]
GER Query on GER Download:Ideal Coordinates CCD File SDF format, chain D [auth Y] MOL2 format, chain D [auth Y] mmCIF format, chain D [auth Y]	D [auth Y]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain D [auth Y] Interactions & Density Focus chain D [auth Y]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth Y] MOL2 format, chain C [auth Y] mmCIF format, chain C [auth Y]	C [auth Y]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth Y] Interactions & Density Focus chain C [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.216 (Depositor), 0.210 (DCC)
R-Value Work: 0.192 (Depositor), 0.187 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.503	α = 90
b = 119.577	β = 90.61
c = 60.723	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-09-01
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: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Structure summary