1VG9 | pdb_00001vg9

The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.250 (Depositor) 
  • R-Value Work: 
    0.206 (Depositor) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1VG9

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

  • 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: 378.3 kDa 
  • Atom Count: 22,604 
  • Modeled Residue Count: 2,688 
  • Deposited Residue Count: 3,340 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rab proteins geranylgeranyltransferase component A 1
A, C, E, G
650Rattus norvegicusMutation(s): 4 
UniProt
Find proteins for P37727 (Rattus norvegicus)
Explore P37727 
Go to UniProtKB:  P37727
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37727
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7
B, D, F, H
185Rattus norvegicusMutation(s): 0 
EC: 3.6.5.2
UniProt
Find proteins for P09527 (Rattus norvegicus)
Explore P09527 
Go to UniProtKB:  P09527
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09527
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
K [auth B],
O [auth D],
S [auth F],
W [auth H]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
P33

Query on P33



Download:Ideal Coordinates CCD File
L [auth B],
P [auth D],
T [auth F],
X [auth H]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
J [auth B],
N [auth D],
R [auth F],
V [auth H]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth B],
M [auth D],
Q [auth F],
U [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.250 (Depositor) 
  • R-Value Work:  0.206 (Depositor) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.392α = 90
b = 144.691β = 90.13
c = 200.086γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ProDCdata collection
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-20
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description