8SH0 | pdb_00008sh0

Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated junction of a telomeric DNA hairpin with a 3'-overhang

• PDB DOI: https://doi.org/10.2210/pdb8SH0/pdb
• NAKB: 8SH0

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-04-13 Released: 2023-08-30 
• Deposition Author(s): Nandakumar, J., Tesmer, V.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD), American Cancer Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Human POT1 protects the telomeric ds-ss DNA junction by capping the 5' end of the chromosome.

Tesmer, V.M., Brenner, K.A., Nandakumar, J.

(2023) Science 381: 771-778

• PubMed: 37590346 
• DOI: https://doi.org/10.1126/science.adi2436
• Primary Citation Related Structures: 
  8SH0, 8SH1


• PubMed Abstract: 
  

  Protection of telomeres 1 (POT1) is the 3' single-stranded overhang-binding telomeric protein that prevents an ataxia telangiectasia and Rad3-related (ATR) DNA damage response (DDR) at chromosome ends. What precludes the DDR machinery from accessing the telomeric double-stranded-single-stranded junction is unknown. We demonstrate that human POT1 binds this junction by recognizing the phosphorylated 5' end of the chromosome. High-resolution crystallographic structures reveal that the junction is capped by POT1 through a "POT-hole" surface, the mutation of which compromises junction protection in vitro and telomeric 5'-end definition and DDR suppression in human cells. Whereas both mouse POT1 paralogs bind the single-stranded overhang, POT1a, not POT1b, contains a POT-hole and binds the junction, which explains POT1a's sufficiency for end protection. Our study shifts the paradigm for DDR suppression at telomeres by highlighting the importance of protecting the double-stranded-single-stranded junction.

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Organizational Affiliation: 
• Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.

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: 40.24 kDa 
• Atom Count: 2,891 
• Modeled Residue Count: 314 
• Deposited Residue Count: 320 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protection of telomeres protein 1	A	300	Homo sapiens	Mutation(s): 0  Gene Names: POT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUX5 (Homo sapiens) Explore Q9NUX5  Go to UniProtKB:  Q9NUX5
PHAROS:  Q9NUX5 GTEx:  ENSG00000128513

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')	B	20	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.23	α = 90
b = 67.23	β = 90
c = 143.373	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Nandakumar, J., Tesmer, V.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120094
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM148276
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R01HD108809
American Cancer Society	United States	RSG-17-037-01-DMC

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release