5ZUU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 


Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30-kDa cleavage and polyadenylation specificity factor 30B [auth A],
C [auth B],
A [auth C],
D
180Arabidopsis thalianaMutation(s): 0 
Gene Names: CPSF30OXT6At1g30460F26G16.5F26G16.6
EC: 3.1.21
UniProt
Find proteins for A9LNK9 (Arabidopsis thaliana)
Explore A9LNK9 
Go to UniProtKB:  A9LNK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9LNK9
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*(6MZ)P*CP*UP*AP*G)-3')E,
F,
G,
H [auth I]
10synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
J [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.108α = 90
b = 74.293β = 90
c = 151.139γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references, Structure summary