7UN7 | pdb_00007un7

DNA Polymerase lambda in complex with a 1nt microhomology substrate

• PDB DOI: https://doi.org/10.2210/pdb7UN7/pdb
• NAKB: 7UN7

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-04-09 Released: 2023-03-29 
• Deposition Author(s): Jamsen, J.A.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Pol lambda promotes microhomology-mediated end-joining.

Chandramouly, G., Jamsen, J., Borisonnik, N., Tyagi, M., Calbert, M.L., Tredinnick, T., Ozdemir, A.Y., Kent, T., Demidova, E.V., Arora, S., Wilson, S.H., Pomerantz, R.T.

(2023) Nat Struct Mol Biol 30: 107-114

• PubMed: 36536104 
• DOI: https://doi.org/10.1038/s41594-022-00895-4
• Primary Citation Related Structures: 
  7UN7


• PubMed Abstract: 
  

  The double-strand break (DSB) repair pathway called microhomology-mediated end-joining (MMEJ) is thought to be dependent on DNA polymerase theta (Polθ) and occur independently of nonhomologous end-joining (NHEJ) factors. An unresolved question is whether MMEJ is facilitated by a single Polθ-mediated end-joining pathway or consists of additional undiscovered pathways. We find that human X-family Polλ, which functions in NHEJ, additionally exhibits robust MMEJ activity like Polθ. Polλ promotes MMEJ in mammalian cells independently of essential NHEJ factors LIG4/XRCC4 and Polθ, which reveals a distinct Polλ-dependent MMEJ mechanism. X-ray crystallography employing in situ photo-induced DSB formation captured Polλ in the act of stabilizing a microhomology-mediated DNA synapse with incoming nucleotide at 2.0 Å resolution and reveals how Polλ performs replication across a DNA synapse joined by minimal base-pairing. Last, we find that Polλ is semisynthetic lethal with BRCA1 and BRCA2. Together, these studies indicate Polλ MMEJ as a distinct DSB repair mechanism.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Spark Therapeutics, Philadelphia, PA, USA.
Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
Kazan Federal University, Kazan, Russian Federation.
Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.27 kDa 
• Atom Count: 2,984 
• Modeled Residue Count: 341 
• Deposited Residue Count: 351 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase lambda	A	329	Homo sapiens	Mutation(s): 1  Gene Names: POLL EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens) Explore Q9UGP5  Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5 GTEx:  ENSG00000166169

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*GP*CP*AP*GP*T)-3')	B [auth T]	7	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*CP*TP*G)-3')	C [auth U]	5	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')	D [auth P]	6	Homo sapiens

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*CP*G)-3')	E [auth D]	4	Homo sapiens

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP (Subject of Investigation/LOI)	F [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	J [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.135	α = 90
b = 62.774	β = 90
c = 140.193	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Jamsen, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	K99ES029572-01
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	4R00ES029572 - 02

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description