7DLZ | pdb_00007dlz

Crystal Structure of Methyltransferase Ribozyme

• PDB DOI: https://doi.org/10.2210/pdb7DLZ/pdb
• NAKB: 7DLZ

• Classification: TRANSFERASE/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-30 Released: 2021-10-27 
• Deposition Author(s): Gan, J.H., Gao, Y.Q., Jiang, H.Y., Chen, D.R., Murchie, A.I.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.266 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences

Jiang, H.Y., Gao, Y.Q., Zhang, L., Chen, D.R., Gan, J.H., Murchie, A.I.H.

(2021) Nat Catal 4: 872-881

• DOI: https://doi.org/10.1038/s41929-021-00685-z

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.89 kDa 
• Atom Count: 4,823 
• Modeled Residue Count: 468 
• Deposited Residue Count: 498 
• 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, C, D	102	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
RNA (45-MER)	E [auth X], F [auth Y]	45	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.266 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.784	α = 90
b = 80.176	β = 91.71
c = 103.296	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-27 
Deposition Author(s): Gan, J.H., Gao, Y.Q., Jiang, H.Y., Chen, D.R., Murchie, A.I.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2016YFA0500604

Revision History  

• Version 1.0: 2021-10-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description