8J6V | pdb_00008j6v

Structure of yeast Arginyl-tRNA-protein transferase 1

• PDB DOI: https://doi.org/10.2210/pdb8J6V/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-04-26 Released: 2023-06-07 
• Deposition Author(s): Yashiro, Y., Tomita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: in silico

Literature

Structure of Arginyl-tRNA-protein transferase 1

Yashiro, Y., Tomita, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Biological Assembly 9  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 9 assigned by authors.

Biological Assembly 10  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 10 assigned by authors.

Biological Assembly 11  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 11 assigned by authors.

Biological Assembly 12  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 12 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 708.87 kDa 
• Atom Count: 45,256 
• Modeled Residue Count: 5,575 
• Deposited Residue Count: 6,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
arginyltransferase	A, B, C [auth D], D [auth F], E, F [auth L], G [auth H], H [auth G], I [auth C], J [auth K], K [auth I], L [auth J]	511	Saccharomyces cerevisiae	Mutation(s): 3  Gene Names: ATE1 EC: 2.3.2.8
UniProt
Find proteins for P16639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16639  Go to UniProtKB:  P16639

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 235.66	α = 90
b = 235.66	β = 90
c = 171.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Yashiro, Y., Tomita, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	LS136
Japan Society for the Promotion of Science (JSPS)	Japan	18H03980
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	26113002
Japan Society for the Promotion of Science (JSPS)	Japan	19K16069
Japan Society for the Promotion of Science (JSPS)	Japan	23H00368
Japan Society for the Promotion of Science (JSPS)	Japan	22K15055

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection