1VG0 | pdb_00001vg0

The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein

PDB DOI: https://doi.org/10.2210/pdb1VG0/pdb

Classification: PROTEIN BINDING/PROTEIN TRANSPORT
Organism(s): Rattus norvegicus
Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2004-04-22 Released: 2004-07-20
Deposition Author(s): Rak, A., Pylypenko, O., Niculae, A., Pyatkov, K., Goody, R.S., Alexandrov, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.233 (Depositor), 0.232 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

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.

Literature

Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease

Rak, A., Pylypenko, O., Niculae, A., Pyatkov, K., Goody, R.S., Alexandrov, K.

(2004) Cell 117: 749-760

PubMed: 15186776 Search on PubMed
DOI: https://doi.org/10.1016/j.cell.2004.05.017
Primary Citation Related Structures:
1VG0, 1VG1, 1VG8, 1VG9

PubMed Abstract:
Members of the RabGDI/REP family serve as multifunctional regulators of the Rab family of GTP binding proteins. Mutations in members of this family, such as REP-1, lead to abnormalities, including progressive retinal degradation (choroideremia) in humans. The crystal structures of the REP-1 protein in complex with monoprenylated or C-terminally truncated Rab7 proteins revealed that Rab7 interacts with the Rab binding platform of REP-1 via an extended interface involving the Switch 1 and 2 regions. The C terminus of the REP-1 molecule functions as a mobile lid covering a conserved hydrophobic patch on the surface of REP-1 that in the complex coordinates the C terminus of Rab proteins. Using semisynthetic fluorescent Rab27A, we demonstrate that although Rab27A can be prenylated by REP-2, this reaction can be effectively inhibited by other Rab proteins, providing a possible explanation for the accumulation of unprenylated Rab27A in choroideremia.

Organizational Affiliation

Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 97.12 kDa
Atom Count: 5,773
Modeled Residue Count: 663
Deposited Residue Count: 857
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab proteins geranylgeranyltransferase component A 1	A	650	Rattus norvegicus	Mutation(s): 4
UniProt
Find proteins for P37727 (Rattus norvegicus) Explore P37727 Go to UniProtKB: P37727
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37727
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-7	B	207	Rattus norvegicus	Mutation(s): 0 EC: 3.6.5.2
UniProt
Find proteins for P09527 (Rattus norvegicus) Explore P09527 Go to UniProtKB: P09527
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09527
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
GER Query on GER Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]