8DHU

Crystal structure of LARP-DM15 from Drosophila melanogaster bound to m7GpppC

• PDB DOI: https://doi.org/10.2210/pdb8DHU/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-28 Released: 2024-01-17 
• Deposition Author(s): Nguyen, E., Berman, A.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Cancer Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.275 
• R-Value Work: 0.220 

Literature

Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution

Nguyen, E., Berman, A.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.92 kDa 
• Atom Count: 2,671 
• Modelled Residue Count: 299 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
La-related protein 1	A, B	152	Drosophila melanogaster	Mutation(s): 0  Gene Names: larp, CG42551
UniProt
Find proteins for Q9VAW5 (Drosophila melanogaster) Explore Q9VAW5  Go to UniProtKB:  Q9VAW5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
91P (Subject of Investigation/LOI)	C [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate C20 H30 N8 O18 P3 MKNQXCMUSBQGFH-KPKSGTNCSA-O
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.275 
• R-Value Work: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.808	α = 90
b = 60.737	β = 90
c = 129.199	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AutoProcess	data reduction
AutoProcess	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Nguyen, E., Berman, A.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
American Cancer Society	United States	--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release