5EAN

Crystal structure of Dna2 in complex with a 5' overhang DNA

• PDB DOI: https://doi.org/10.2210/pdb5EAN/pdb
• NAKB: 5EAN

• Classification: Hydrolase/DNA
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-10-16 Released: 2015-11-18 
• Deposition Author(s): Zhou, C., Pourmal, S., Pavletich, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.246 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

Zhou, C., Pourmal, S., Pavletich, N.P.

(2015) Elife 4

• PubMed: 26491943 
• DOI: https://doi.org/10.7554/eLife.09832
• Primary Citation of Related Structures:  
  5EAN, 5EAW, 5EAX, 5EAY


• PubMed Abstract: 
  

  The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124.64 kDa 
• Atom Count: 8,652 
• Modelled Residue Count: 1,066 
• Deposited Residue Count: 1,074 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication ATP-dependent helicase/nuclease DNA2	A	1,059	Mus musculus	Mutation(s): 0  Gene Names: Dna2, Dna2l, Kiaa0083 EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for Q6ZQJ5 (Mus musculus) Explore Q6ZQJ5  Go to UniProtKB:  Q6ZQJ5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')	B	15	Mus musculus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.246 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.153	α = 90
b = 118.488	β = 90
c = 149.26	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Zhou, C., Pourmal, S., Pavletich, N.P.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description