8SWC | pdb_00008swc

RNase H complex with ASO (OOO) and RNA

• PDB DOI: https://doi.org/10.2210/pdb8SWC/pdb
• NAKB: 8SWC

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-05-18 Released: 2024-06-19 
• Deposition Author(s): Cho, Y.-J., Iwamoto, N.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RNase H/RNA/PO-ASO complex at an atomic level

Iwamoto, N., Cho, Y.-J.

To be published.

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

Macromolecule Content 

• Total Structure Weight: 46.62 kDa 
• Atom Count: 2,052 
• Modeled Residue Count: 189 
• Deposited Residue Count: 334 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H1	A	294	Homo sapiens	Mutation(s): 1  Gene Names: RNASEH1, RNH1 EC: 3.1.26.4
UniProt & NIH Common Fund Data Resources
Find proteins for O60930 (Homo sapiens) Explore O60930  Go to UniProtKB:  O60930
PHAROS:  O60930 GTEx:  ENSG00000171865

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3')	B	20	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
PO ASO	C	20	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	D [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	E [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.617	α = 90
b = 100.617	β = 90
c = 82.092	γ = 120

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: 2024-06-19 
Deposition Author(s): Cho, Y.-J., Iwamoto, N.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release