8I3F: Rco1-Eaf3 with peptide of histone H3 N-terminal

Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal. Determined by X-ray diffraction at 1.62 Å resolution. Released 31 May 2023.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 2,737
Mol. weight: 35.5 kDa
Ligands: ZN
Released: 31 May 2023

Explore 8I3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I3F contains 18 α-helices and 10 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	226-240	15
β-strand	244-246	3	1
β-strand	253	1	2
α-helix	254-267	14
α-helix	272-296	25
α-helix	302-315	14
α-helix	322-324	3
β-strand	327	1	2
α-helix	328-343	16
α-helix	349-368	20
α-helix	370-374	5
β-strand	387-389	3	1
α-helix	390-391	2
α-helix	392-399	8

Chain B: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	263	1	3
β-strand	271-274	4	3
β-strand	281-283	3	3
α-helix	284-286	3
α-helix	290-292	3
α-helix	304-313	10
α-helix	319-329	11
α-helix	331-336	6
α-helix	337-342	6
α-helix	343-345	3
α-helix	355-358	4
β-strand	365-366	2	4
β-strand	372-373	2	4

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromatin modification-related protein EAF3	A	protein	183	Saccharomyces cerevisiae	Q12432 (AlphaFold model)
RCO1 isoform 1	B	protein	118	Saccharomyces cerevisiae	Q04779 (AlphaFold model)
Histone H3	C	protein	6	Saccharomyces cerevisiae	P61830 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8I3F_1 Chromatin modification-related protein EAF3 (chains A)
PKISLQIPIKLKSVLVDDWEYVTKDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQ
LSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISV
LPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGV
ALG

Sequence of entity 2 (B), FASTA

>8I3F_2 RCO1 isoform 1 (chains B)
ENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMA
TLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDE

Sequence of entity 3 (C), FASTA

>8I3F_3 Histone H3 (chains C)
ARTKQT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Molecular basis for Eaf3-mediated assembly of Rpd3S and NuA4. Chen, Z., Lundy, T., Zhu, Z. et al. Cell Discov (2023) 9:51-51. DOI 10.1038/s41421-023-00565-9 · PubMed

Other PDB entries of the same protein (UniProt Q12432 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3E9F 1.8 Å, Crystal structure short-form (residue1-113) of Eaf3 chromo domain
8I3G 2.4 Å, Crystal structure of Eaf3-Eaf7 complex
3E9G 2.5 Å, Crystal structure long-form (residue1-124) of Eaf3 chromo domain
7YI1 2.8 Å, Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome
8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
8KD3 2.9 Å, Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
8KD5 2.9 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
8KD4 2.93 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
8HXX 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3S
8KD2 3.02 Å, Rpd3S in complex with 187bp nucleosome
8KD6 3.07 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
8KD7 3.09 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA

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