8SWB | pdb_00008swb

RNase H complex with streopure ASO and RNA

• PDB DOI: https://doi.org/10.2210/pdb8SWB/pdb
• NAKB: 8SWB

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-18 Released: 2024-05-22 
• 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: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RNase H/RNA/PS-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: 30.11 kDa 
• Atom Count: 2,226 
• Modeled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H1	A	149	Homo sapiens	Mutation(s): 0  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
DNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*AP*(SC)P*(SC)P*(RC)P*(AS)P*(SC)P*(PST))-R(P*(6OO)P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3')	C [auth D]	20	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.545	α = 90
b = 52.939	β = 90
c = 106.008	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: 2024-05-22 
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: 2024-05-22
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary