8DEI | pdb_00008dei

Structure of the Cac1 KER domain

PDB DOI: https://doi.org/10.2210/pdb8DEI/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-20 Released: 2023-07-05
Deposition Author(s): Rosas, R., Churchill, M.E.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.282 (Depositor), 0.283 (DCC)
R-Value Work:
0.233 (Depositor), 0.235 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function.

Rosas, R., Aguilar, R.R., Arslanovic, N., Seck, A., Smith, D.J., Tyler, J.K., Churchill, M.E.A.

(2023) Elife 12

PubMed: 37432722 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.83538
Primary Citation Related Structures:
8DEI

PubMed Abstract:
The histone chaperone chromatin assembly factor 1 (CAF-1) deposits two nascent histone H3/H4 dimers onto newly replicated DNA forming the central core of the nucleosome known as the tetrasome. How CAF-1 ensures there is sufficient space for the assembly of tetrasomes remains unknown. Structural and biophysical characterization of the lysine/glutamic acid/arginine-rich (KER) region of CAF-1 revealed a 128-Å single alpha-helix (SAH) motif with unprecedented DNA-binding properties. Distinct KER sequence features and length of the SAH drive the selectivity of CAF-1 for tetrasome-length DNA and facilitate function in budding yeast. In vivo, the KER cooperates with the DNA-binding winged helix domain in CAF-1 to overcome DNA damage sensitivity and maintain silencing of gene expression. We propose that the KER SAH links functional domains within CAF-1 with structural precision, acting as a DNA-binding spacer element during chromatin assembly.

Organizational Affiliation

Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, United States.

Macromolecule Content

Total Structure Weight: 223.15 kDa
Atom Count: 14,713
Modeled Residue Count: 1,870
Deposited Residue Count: 1,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion	A, B, C, D	490	Escherichia coli, Saccharomyces cerevisiae This entity is chimeric	Mutation(s): 0 Gene Names: malE, malE_1, malE_2, RLF2, CAC1, YPR018W, YP9531.12
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for Q12495 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12495 Go to UniProtKB: Q12495
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q12495 P0AEX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain J [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C]	E [auth B], F [auth B], I [auth C], J [auth C], K [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.282 (Depositor), 0.283 (DCC)
R-Value Work: 0.233 (Depositor), 0.235 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.586	α = 90
b = 165.249	β = 96.475
c = 116.149	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Rosas, R.

Churchill, M.E.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM135604

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Structure summary
Version 1.2: 2023-10-25
Changes: Refinement description
Version 1.3: 2024-02-14
Changes: Database references