7PV5 | pdb_00007pv5

RBD domain of D. melanogaster tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A)

• PDB DOI: https://doi.org/10.2210/pdb7PV5/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-01 Released: 2023-04-19 
• Deposition Author(s): Witzenberger, M., Janowski, R., Niessing, D.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal structure of the RNA-recognition motif of Drosophila melanogaster tRNA (uracil-5-)-methyltransferase homolog A

Witzenberger, M., Janowski, R., Niessing, D.

(2024) Acta Crystallogr F Struct Biol Commun 80

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.

Macromolecule Content 

• Total Structure Weight: 21.66 kDa 
• Atom Count: 1,552 
• Modeled Residue Count: 152 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FI05218p	A, B	81	Drosophila melanogaster	Mutation(s): 0  EC: 2.1.1.35
UniProt
Find proteins for Q9VVV7 (Drosophila melanogaster) Explore Q9VVV7  Go to UniProtKB:  Q9VVV7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], CA [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AA [auth A], AB [auth B], BA [auth A], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth B], IB [auth B], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
85L	A, B	L-PEPTIDE LINKING	C3 H6 Au2 Cl2 N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.41	α = 90
b = 41.89	β = 110.8
c = 48.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Witzenberger, M., Janowski, R., Niessing, D.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2024-07-10
  Changes: Data collection, Non-polymer description, Structure summary
• Version 2.1: 2024-10-23
  Changes: Structure summary