6VRD | pdb_00006vrd

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

• PDB DOI: https://doi.org/10.2210/pdb6VRD/pdb
• NAKB: 6VRD

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-02-07 Released: 2021-02-10 
• Deposition Author(s): Cho, Y.-J., Butler, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

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

Cho, Y.-J., Butler, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.96 kDa 
• Atom Count: 2,513 
• 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
RNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC)P*(PST)P*(SC)P*(AS)P*(SC)P*(SC)P*(SC)P*(AS)P*(SC)P*(PST))-R(P*(6OO)P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3')	C	20	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.76	α = 90
b = 53.03	β = 90
c = 106.477	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Cho, Y.-J., Butler, D.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Database references, Structure summary