7YBF: Inner membrane protein Sad1

Name: PDB 7YBF: Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B
Published: 2024-01-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B. Determined by X-ray diffraction at 2.15 Å resolution. Released 3 Jan 2024.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Schizosaccharomyces pombe
Chains: 3
Atoms: 2,951
Mol. weight: 43.44 kDa
Released: 3 Jan 2024

Explore 7YBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YBF contains 19 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: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	1
β-strand	58	1	2
α-helix	59-86	28
β-strand	91-92	2	3
α-helix	94-104	11
α-helix	107-126	20
α-helix	134-138	5
α-helix	144-153	10
β-strand	159-160	2	3
α-helix	163-189	27
β-strand	194-195	2	1
α-helix	197-206	10
α-helix	208-214	7

Chain B: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	4
α-helix	59-86	28
β-strand	91-92	2	5
α-helix	94-104	11
α-helix	107-126	20
α-helix	134-137	4
α-helix	144-153	10
β-strand	159-160	2	5
α-helix	163-189	27
β-strand	194-195	2	4
α-helix	197-206	10
α-helix	208-214	7

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	117	1	2
α-helix	118	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2B-alpha,Histone H2A-beta	A, B	protein	189	Schizosaccharomyces pombe	P04910 (AlphaFold model), P04913 (AlphaFold model)
Spindle pole body-associated protein sad1	C	protein	17	Schizosaccharomyces pombe	Q09825 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7YBF_1 Histone H2B-alpha,Histone H2A-beta (chains A, B)
NRKETYSSYIYKVLKQVHPDTGISNQAMRILNSFVNDIFERIATEASKLAAYNKKSTISS
REIQTAVRLILPGELAKHAVTEGTKSVTKYSSSAQSAQSRSAKAGLAFPVGRVHRLLRKG
NYAQRVGAGAPVYLAAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL
GHVTIAQGG

Sequence of entity 2 (C), FASTA

>7YBF_2 Spindle pole body-associated protein sad1 (chains C)
ESDGDDEEFVNEEYENS

Primary citation

The SUN-family protein Sad1 mediates heterochromatin spatial organization through interaction with histone H2A-H2B. Sun, W., Dong, Q., Li, X. et al. Nat Commun (2024) 15:4322-4322. DOI 10.1038/s41467-024-48418-7 · PubMed

Other PDB entries of the same protein (UniProt P04910 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P0L 1.97 Å, Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide

Browse structure collections

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