6J6X | pdb_00006j6x

Crystal structure of apo GGTaseIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 
    0.297 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus.

Shirakawa, R.Goto-Ito, S.Goto, K.Wakayama, S.Kubo, H.Sakata, N.Trinh, D.A.Yamagata, A.Sato, Y.Masumoto, H.Cheng, J.Fujimoto, T.Fukai, S.Horiuchi, H.

(2020) EMBO J 39: e104120-e104120

  • DOI: https://doi.org/10.15252/embj.2019104120
  • Primary Citation of Related Structures:  
    6J6X, 6J74, 6J7F, 6J7X

  • PubMed Abstract: 

    Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein prenyltransferase alpha subunit repeat-containing protein 1366Homo sapiensMutation(s): 0 
Gene Names: PTAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6K3 (Homo sapiens)
Explore Q7Z6K3 
Go to UniProtKB:  Q7Z6K3
PHAROS:  Q7Z6K3
GTEx:  ENSG00000188647 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6K3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit beta336Homo sapiensMutation(s): 0 
Gene Names: RABGGTBGGTB
EC: 2.5.1.60
UniProt & NIH Common Fund Data Resources
Find proteins for P53611 (Homo sapiens)
Explore P53611 
Go to UniProtKB:  P53611
PHAROS:  P53611
GTEx:  ENSG00000137955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53611
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free:  0.297 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.54α = 90
b = 88.54β = 90
c = 647.581γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanCREST JPMJCR12M5
Japan Society for the Promotion of ScienceJapanKAKENHI 16K08574
Japan Society for the Promotion of ScienceJapanKAKENHI 16H05148

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary
  • Version 1.3: 2025-05-28
    Changes: Database references