5OQD | pdb_00005oqd

PHD2 and winged-helix domain of Polycomblike

PDB DOI: https://doi.org/10.2210/pdb5OQD/pdb

Classification: GENE REGULATION
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-11 Released: 2017-11-01
Deposition Author(s): Choi, J., Benda, C., Mueller, J.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.278 (Depositor), 0.285 (DCC)
R-Value Work:
0.236 (Depositor), 0.249 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation.

Choi, J., Bachmann, A.L., Tauscher, K., Benda, C., Fierz, B., Muller, J.

(2017) Nat Struct Mol Biol 24: 1039-1047

PubMed: 29058710 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.3488
Primary Citation Related Structures:
5OQD

PubMed Abstract:
Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27 to mark genes for repression. We measured the dynamics of PRC2 binding on recombinant chromatin and free DNA at the single-molecule level using total internal reflection fluorescence (TIRF) microscopy. PRC2 preferentially binds free DNA with multisecond residence time and midnanomolar affinity. PHF1, a PRC2 accessory protein of the Polycomblike family, extends PRC2 residence time on DNA and chromatin. Crystallographic and functional studies reveal that Polycomblike proteins contain a winged-helix domain that binds DNA in a sequence-nonspecific fashion. DNA binding by this winged-helix domain accounts for the prolonged residence time of PHF1-PRC2 on chromatin and makes it a more efficient H3K27 methyltranferase than PRC2 alone. Together, these studies establish that interactions with DNA provide the predominant binding affinity of PRC2 for chromatin. Moreover, they reveal the molecular basis for how Polycomblike proteins stabilize PRC2 on chromatin and stimulate its activity.

Organizational Affiliation

Max Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 153.92 kDa
Atom Count: 9,058
Modeled Residue Count: 1,121
Deposited Residue Count: 1,254
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein Pcl	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F	209	Drosophila melanogaster	Mutation(s): 0 Gene Names: Pcl, CG5109
UniProt
Find proteins for Q24459 (Drosophila melanogaster) Explore Q24459 Go to UniProtKB: Q24459
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q24459
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	O [auth C], T [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain O [auth C] Focus chain T [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain L [auth A] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain M [auth C] SDF format, chain K [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain M [auth C] MOL2 format, chain K [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain L [auth A] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain M [auth C] mmCIF format, chain K [auth A]	G [auth B] H [auth B] K [auth A] L [auth A] M [auth C] G [auth B], H [auth B], K [auth A], L [auth A], M [auth C], N [auth C], R [auth D], S [auth D], U [auth E], V [auth E], W [auth F], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain Y [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth F] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain Y [auth F]	I [auth B], J [auth B], P [auth C], Q [auth C], Y [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain Y [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain Y [auth F]