1LTX | pdb_00001ltx

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

• PDB DOI: https://doi.org/10.2210/pdb1LTX/pdb

• Classification: Transferase/Protein binding
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2002-05-21 Released: 2003-05-21 
• Deposition Author(s): Pylypenko, O., Rak, A., Reents, R., Niculae, A., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.272 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase

Pylypenko, O., Rak, A., Reents, R., Niculae, A., Sidorovitch, V., Cioaca, M.D., Bessolitsyna, E., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

(2003) Mol Cell 11: 483-494

• PubMed: 12620235 
• DOI: https://doi.org/10.1016/s1097-2765(03)00044-3
• Primary Citation Related Structures: 
  1LTX


• PubMed Abstract: 
  

  Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies.

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Organizational Affiliation: 
• Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 175.08 kDa 
• Atom Count: 10,874 
• Modeled Residue Count: 1,352 
• Deposited Residue Count: 1,552 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT	A	567	Rattus norvegicus	Mutation(s): 0  EC: 2.5.1 (PDB Primary Data), 2.5.1.60 (UniProt)
UniProt
Find proteins for Q08602 (Rattus norvegicus) Explore Q08602  Go to UniProtKB:  Q08602

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT	B	331	Rattus norvegicus	Mutation(s): 0  EC: 2.5.1 (PDB Primary Data), 2.5.1.60 (UniProt)
UniProt
Find proteins for Q08603 (Rattus norvegicus) Explore Q08603  Go to UniProtKB:  Q08603

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab Escort Protein 1	C [auth R]	650	Rattus norvegicus	Mutation(s): 3
UniProt
Find proteins for P37727 (Rattus norvegicus) Explore P37727  Go to UniProtKB:  P37727

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AAAA	D [auth P]	4	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAR	G [auth P]	FARNESYL C15 H26 JXBSHSBNOVLGHF-BUJBXKITSA-N
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth R]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.272 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.7	α = 90
b = 197.3	β = 112.8
c = 85.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-21 
Deposition Author(s): Pylypenko, O., Rak, A., Reents, R., Niculae, A., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

Revision History  

• Version 1.0: 2003-05-21
  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: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description