9C6L

Yasminevirus c12orf29, a 5' to 3' RNA ligase

• PDB DOI: https://doi.org/10.2210/pdb9C6L/pdb

• Classification: LIGASE
• Organism(s): Yasminevirus sp. GU-2018
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-07 Released: 2024-10-02 
• Deposition Author(s): Hu, Y., Lopez, V.A., Tagliabracci, V.S., Tomchick, D.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation, Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation

Hu, Y., Lopez, V.A., Xu, H., Song, B., Servage, K.A., Sakurai, M., Jones, B.T., Mendell, J.T., Wang, T., Wu, J., Lambowitz, A.M., Tomchick, D.R., Pawlowski, K., Tagliabracci, V.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 186.06 kDa 
• Atom Count: 11,413 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA ligase1	A, B, C, D, E, F	277	Yasminevirus sp. GU-2018	Mutation(s): 0  Gene Names: YASMINEVIRUS_1364
UniProt
Find proteins for A0A5K0UB63 (Yasminevirus sp. GU-2018) Explore A0A5K0UB63  Go to UniProtKB:  A0A5K0UB63

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	G [auth A], M [auth B], O [auth C], R [auth D], T [auth E], W [auth F]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG	L [auth A], N [auth B], Q [auth C], S [auth D], U [auth E], V [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth A], I [auth A], J [auth A], K [auth A], P [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.897	α = 90
b = 84.221	β = 106.875
c = 115.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Hu, Y., Lopez, V.A., Tagliabracci, V.S., Tomchick, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM137419
Robert A. Welch Foundation	United States	I-1911
Robert A. Welch Foundation	United States	I-2088
Robert A. Welch Foundation	United States	I-1961
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release