2BCG | pdb_00002bcg

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

(2006) EMBO J 25: 13-23

PubMed Abstract:
In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic controllers that associate with their targeted membranes via C-terminally conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general and essential regulator of Rab recycling that extracts prenylated Rab proteins from membranes at the end of their cycle of activity and facilitates their delivery to the donor membranes. Here, we present the structure of a complex between GDI and a doubly prenylated Rab protein. We show that one geranylgeranyl residue is deeply buried in a hydrophobic pocket formed by domain II of GDI, whereas the other lipid is more exposed to solvent and is skewed across several atoms of the first moiety. Based on structural information and biophysical measurements, we propose mechanistic and thermodynamic models for GDI and Rab escort protein-mediated interaction of RabGTPase with intracellular membranes.

Organizational Affiliation

Macromolecule Content

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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 Gene Names: GDI1
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
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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): 1 Gene Names: YPT1 Membrane Entity: Yes
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

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain F [auth Y] MOL2 format, chain F [auth Y] mmCIF format, chain F [auth Y]	F [auth Y]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth Y] Interactions & Density Focus chain F [auth Y]
GER Query on GER Download:Ideal Coordinates CCD File SDF format, chain C [auth G] SDF format, chain D [auth G] MOL2 format, chain C [auth G] MOL2 format, chain D [auth G] mmCIF format, chain C [auth G] mmCIF format, chain D [auth G]	C [auth G], D [auth G]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain C [auth G] Focus chain D [auth G] Interactions & Density Focus chain C [auth G] Focus chain D [auth G]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain G [auth Y] MOL2 format, chain G [auth Y] mmCIF format, chain G [auth Y]	G [auth Y]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth Y] Interactions & Density Focus chain G [auth Y]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth Y] Interactions & Density Focus chain E [auth Y]