4HLQ

Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Catalytic mechanism of a mammalian Rab-RabGAP complex in atomic detail.

Gavriljuk, K.Gazdag, E.M.Itzen, A.Kotting, C.Goody, R.S.Gerwert, K.

(2012) Proc Natl Acad Sci U S A 109: 21348-21353

  • DOI: 10.1073/pnas.1214431110
  • Primary Citation of Related Structures:  
    4HL4, 4HLQ

  • PubMed Abstract: 
  • Rab GTPases, key regulators of vesicular transport, hydrolyze GTP very slowly unless assisted by Rab GTPase-activating proteins (RabGAPs). Dysfunction of RabGAPs is involved in many diseases. By combining X-ray structure analysis and time-resolved FTIR spectroscopy we reveal here the detailed molecular reaction mechanism of a complex between human Rab and RabGAP at the highest possible spatiotemporal resolution and in atomic detail ...

    Rab GTPases, key regulators of vesicular transport, hydrolyze GTP very slowly unless assisted by Rab GTPase-activating proteins (RabGAPs). Dysfunction of RabGAPs is involved in many diseases. By combining X-ray structure analysis and time-resolved FTIR spectroscopy we reveal here the detailed molecular reaction mechanism of a complex between human Rab and RabGAP at the highest possible spatiotemporal resolution and in atomic detail. A glutamine residue of Rab proteins (cis-glutamine) that is essential for intrinsic activity is less important in the GAP-activated reaction. During generation of the RabGAP·Rab:GTP complex, there is a rapid conformational change in which the cis-glutamine is replaced by a glutamine from RabGAP (trans-glutamine); this differs from the RasGAP mechanism, where the cis-glutamine is also important for GAP catalysis. However, as in the case of Ras, a trans-arginine is also recruited to complete the active center during this conformational change. In contrast to the RasGAP mechanism, an accumulation of a state in which phosphate is bound is not observed, and bond breakage is the rate-limiting step. The movement of trans-glutamine and trans-arginine into the catalytic site and bond breakage during hydrolysis are monitored in real time. The combination of X-ray structure analysis and time-resolved FTIR spectroscopy provides detailed insight in the catalysis of human Rab GTPases.


    Organizational Affiliation

    Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TBC1 domain family member 20A, C, E, G, I305Homo sapiensMutation(s): 0 
Gene Names: TBC1D20C20orf140
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BZ9 (Homo sapiens)
Explore Q96BZ9 
Go to UniProtKB:  Q96BZ9
PHAROS:  Q96BZ9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-1BB, D, F, H, J175Homo sapiensMutation(s): 0 
Gene Names: RAB1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U4 (Homo sapiens)
Explore Q9H0U4 
Go to UniProtKB:  Q9H0U4
PHAROS:  Q9H0U4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
CA [auth J], M [auth B], Q [auth D], V [auth F], Y [auth H]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth I], K [auth A], O [auth C], S [auth E], T [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BEF
Query on BEF

Download Ideal Coordinates CCD File 
DA [auth J], N [auth B], R [auth D], W [auth F], Z [auth H]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth J], L [auth B], P [auth D], U [auth F], X [auth H]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.17α = 90
b = 118.64β = 90
c = 290.11γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release