5ZUU | pdb_00005zuu

Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA

• PDB DOI: https://doi.org/10.2210/pdb5ZUU/pdb
• NAKB: 5ZUU

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Arabidopsis thaliana, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-08 Released: 2019-05-15 
• Deposition Author(s): Wu, B., Nie, H., Li, S., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.256 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis.

Hou, Y., Sun, J., Wu, B., Gao, Y., Nie, H., Nie, Z., Quan, S., Wang, Y., Cao, X., Li, S.

(2021) Mol Plant 

• DOI: https://doi.org/10.1016/j.molp.2021.01.013

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.76 kDa 
• Atom Count: 5,701 
• Modeled Residue Count: 650 
• Deposited Residue Count: 760 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
30-kDa cleavage and polyadenylation specificity factor 30	A [auth C], B [auth A], C [auth B], D	180	Arabidopsis thaliana	Mutation(s): 0  EC: 3.1.21
UniProt
Find proteins for A9LNK9 (Arabidopsis thaliana) Explore A9LNK9  Go to UniProtKB:  A9LNK9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')	E, F, G, H [auth I]	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	J [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.256 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.108	α = 90
b = 74.293	β = 90
c = 151.139	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Wu, B., Nie, H., Li, S., Patel, D.J.

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description