6J7X

Complex of GGTaseIII, farnesyl-Ykt6, and GGPP

• PDB DOI: https://doi.org/10.2210/pdb6J7X/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-18 Released: 2020-01-22 
• Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP

Goto-Ito, S., Shirakawa, R., Fukai, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.3 kDa 
• Atom Count: 6,430 
• Modelled Residue Count: 795 
• Deposited Residue Count: 861 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein prenyltransferase alpha subunit repeat-containing protein 1	A	327	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit beta	B	336	Homo sapiens	Mutation(s): 0  Gene Names: RABGGTB, GGTB 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptobrevin homolog YKT6	C	198	Homo sapiens	Mutation(s): 0  Gene Names: YKT6 EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15498 (Homo sapiens) Explore O15498  Go to UniProtKB:  O15498
PHAROS:  O15498 GTEx:  ENSG00000106636

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GRG (Subject of Investigation/LOI)	D [auth B]	GERANYLGERANYL DIPHOSPHATE C20 H36 O7 P2 OINNEUNVOZHBOX-QIRCYJPOSA-N
FMT	E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.169	α = 90
b = 119.169	β = 90
c = 211.006	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.

---

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	CREST JPMJCR12M5
Japan Society for the Promotion of Science	Japan	KAKENHI 16K08574
Japan Society for the Promotion of Science	Japan	KAKENHI 16H05148

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description