7QR3 | pdb_00007qr3

Chimpanzee CPEB3 HDV-like ribozyme

• PDB DOI: https://doi.org/10.2210/pdb7QR3/pdb
• NAKB: 7QR3

• Classification: RNA
• Organism(s): Homo sapiens, Pan troglodytes
• Expression System: Expression vector pET-mod
• Mutation(s): No 


• Deposited: 2022-01-10 Released: 2022-10-26 
• Deposition Author(s): Przytula-Mally, A.I., Engilberge, S., Johannsen, S., Olieric, V., Masquida, B., Sigel, R.K.O.
• Funding Organization(s): University of Zurich, Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.277 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes

Przytula-Mally, A.I., Engilberge, S., Johannsen, S., Olieric, V., Masquida, B., Sigel, R.K.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.09.22.508989

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.63 kDa 
• Atom Count: 4,497 
• Modeled Residue Count: 320 
• Deposited Residue Count: 320 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	A, B	91	Homo sapiens	Mutation(s): 0  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012 GTEx:  ENSG00000077312

Entity ID: 2
Molecule	Chains	Length	Organism	Image
chimpanzee CPEB3 ribozyme	C, D	69	Pan troglodytes

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth A], F [auth B], H [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.277 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.254	α = 90
b = 135.916	β = 90
c = 83.254	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Przytula-Mally, A.I., Engilberge, S., Johannsen, S., Olieric, V., Masquida, B., Sigel, R.K.O.

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Funding Organization	Location	Grant Number
University of Zurich	Switzerland	FK-18-097
Agence Nationale de la Recherche (ANR)	Switzerland	ANR-10-IDEX-0002
Agence Nationale de la Recherche (ANR)	Switzerland	ANR-17-EUR-0023

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description