Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142758.05 
• Atom Count: 7979 
• Residue Count: 1092 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

5T9J

Crystal Structure of human GEN1 in complex with Holliday junction DNA in the upper interface

• DOI: 10.2210/pdb5T9J/pdb
• NDB: 5T9J

• Classification: HYDROLASE
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2016-09-09 Released: 2016-09-21 
• Deposition Author(s): Lee, S.-H., Biertumpfel, C.
• Funding Organization(s): Max Planck Society 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00013 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 

Literature

Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage.

Lee, S.H., Princz, L.N., Klugel, M.F., Habermann, B., Pfander, B., Biertumpfel, C.

(2015) Elife 4: --

• PubMed: 26682650 
• DOI: 10.7554/eLife.12256


• PubMed Abstract: 
  

Holliday junctions (HJs) are key DNA intermediates in homologous recombination. They link homologous DNA strands and have to be faithfully removed for proper DNA segregation and genome integrity. Here, we present the crystal structure of human HJ resolvase GEN1 complexed with DNA at 3.0 Å resolution. The GEN1 core is similar to other Rad2/XPG nucleases. However, unlike other members of the superfamily, GEN1 contains a chromodomain as an additional DNA interaction site. Chromodomains are known for their chromatin-targeting function in chromatin remodelers and histone(de)acetylases but they have not previously been found in nucleases. The GEN1 chromodomain directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. Structure-guided mutations in vitro and in vivo in yeast validated our mechanistic findings. Our study provides the missing structure in the Rad2/XPG family and insights how a well-conserved nuclease core acquires versatility in recognizing diverse substrates for DNA repair and maintenance.

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Organizational Affiliation: 

Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Flap endonuclease GEN homolog 1	A, B	506	Homo sapiens	Mutation(s): 1  Gene Names: GEN1 EC: 3.1.-.-
Find proteins for Q17RS7 (Homo sapiens) Go to Gene View: GEN1 Go to UniProtKB:  Q17RS7

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DGP*DC)-3')	C	20	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(*DGP*DCP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DT)-3')	D	20	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-D(*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DCP*DTP*DC)-3')	E	20	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (5'-D(*DGP*DAP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DAP*DTP*DTP*DC)-3')	F	20	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00013 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 
• Space Group: P 3₂

Unit Cell:

Length (Å)	Angle (°)
a = 86.940	α = 90.00
b = 86.940	β = 90.00
c = 200.724	γ = 120.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-09 
• Released Date: 2016-09-21 
• Deposition Author(s): Lee, S.-H., Biertumpfel, C.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	Max Planck Research Group Leader Program

Revision History 

• Version 1.0: 2016-09-21
  Type: Initial release