5Z8N: Chromatin remodeling protein EBS

Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide. Determined by X-ray diffraction at 3.1 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Arabidopsis thaliana
Chains: 6
Atoms: 4,544
Mol. weight: 73.11 kDa
Ligands: ZN
Released: 25 Jul 2018

Explore 5Z8N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z8N contains 20 α-helices and 47 β-strands across 6 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: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	1
β-strand	21-23	3	2
β-strand	30-32	3	2
β-strand	36-39	4	1
α-helix	47-48	2
β-strand	49-58	10	1
β-strand	64-72	9	1
α-helix	73	1
β-strand	89-100	12	1
α-helix	101-103	3
β-strand	104-112	9	1
α-helix	113-117	5
β-strand	126-134	9	1
β-strand	139-141	3	1
β-strand	147-148	2	3
β-strand	153-154	2	3
α-helix	155	1
β-strand	162-163	2	4
β-strand	170-171	2	4
α-helix	174-176	3
α-helix	180-183	4
α-helix	192-194	3

Chain B: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	5
β-strand	22-23	2	6
β-strand	30-31	2	6
β-strand	36-39	4	5
β-strand	44	1	7
β-strand	46	1	7
α-helix	47-48	2
β-strand	49-58	10	5
β-strand	64-72	9	5
α-helix	73	1
β-strand	89-100	12	5
α-helix	101-103	3
β-strand	104-111	8	5
α-helix	113-118	6
β-strand	126-133	8	5
β-strand	140-141	2	5
β-strand	147-148	2	8
β-strand	153-154	2	8
β-strand	161-163	3	9
β-strand	170-171	2	9
α-helix	180-185	6

Chain C: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	10
β-strand	22-23	2	11
α-helix	24	1
β-strand	30-31	2	11
β-strand	36-39	4	10
α-helix	46-48	3
β-strand	49-58	10	10
β-strand	64-72	9	10
α-helix	73	1
β-strand	89-100	12	10
α-helix	101-103	3
β-strand	104-111	8	10
α-helix	113-118	6
β-strand	126-133	8	10
β-strand	140-141	2	10
β-strand	147-148	2	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	161-163	3	13
β-strand	170-171	2	13
α-helix	180-185	6

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	4

Chains Q and R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromatin remodeling protein EBS	A, B, C	protein	199	Arabidopsis thaliana	F4JL28 (AlphaFold model)
H3K4me2 peptide	P, Q, R	protein	15	Arabidopsis thaliana	P59226 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>5Z8N_1 Chromatin remodeling protein EBS (chains A, B, C)
MAKTRPGVASKIKTGRKELDSYTIKGTNKVVRAGDCVLMRPSDAGKPPYVARVEKIEADA
RNNVKVHCRWYYRPEESLGGRRQFHGAKELFLSDHFDVQSAHTIEGKCIVHTFKNYTRLE
NVGAEDYYCRFEYKAATGAFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWYHPACVGMTI
EEAKKLDHFVCAECSSDDD

Sequence of entity 2 (P, Q, R), FASTA

>5Z8N_2 H3K4me2 peptide (chains P, Q, R)
ARTKQTARKSTGGKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Yang, Z., Qian, S., Scheid, R.N. et al. Nat Genet (2018) 50:1247-1253. DOI 10.1038/s41588-018-0187-8 · PubMed

Other PDB entries of the same protein (UniProt F4JL28 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5Z8L 2.0 Å, crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide

Browse structure collections

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