7DLX: H2AM4>Z-H2B

crystal structure of H2AM4>Z-H2B. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Jun 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Saccharomyces cerevisiae (strain RM11-1a)
Chains: 8
Atoms: 10,856
Mol. weight: 180.27 kDa
Released: 16 Jun 2021

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

Secondary structure: helices and β-sheets

7DLX contains 72 α-helices and 32 β-strands across 8 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, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	1
α-helix	59-86	28
β-strand	91-92	2	2
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-152	5
α-helix	158-166	9
β-strand	173-174	2	2
α-helix	176-203	28
β-strand	208-209	2	1
α-helix	211-219	9
α-helix	222-228	7

Chain B: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	3
α-helix	59-86	28
β-strand	91-92	2	4
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-151	4
α-helix	158-166	9
β-strand	173-174	2	4
α-helix	176-203	28
β-strand	208-209	2	3
α-helix	211-219	9
α-helix	222-228	7

Chain C: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-49	9
β-strand	56-57	2	5
α-helix	59-86	28
β-strand	91-92	2	6
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-151	4
α-helix	158-166	9
β-strand	173-174	2	6
α-helix	176-202	27
β-strand	208-209	2	5
α-helix	211-220	10
α-helix	222-228	7

Chain D: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-49	9
β-strand	56-57	2	7
α-helix	59-86	28
β-strand	91-92	2	8
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-151	4
α-helix	158-167	10
β-strand	173-174	2	8
α-helix	176-203	28
β-strand	208-209	2	7
α-helix	211-220	10
α-helix	222-225	4

Chain E: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	9
α-helix	59-86	28
β-strand	91-92	2	10
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-151	4
α-helix	158-164	7
β-strand	173-174	2	10
α-helix	176-202	27
β-strand	208-209	2	9
α-helix	211-219	9
α-helix	222-227	6

Chain F: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	42-49	8
β-strand	56-57	2	11
α-helix	59-86	28
β-strand	91-92	2	12
α-helix	94-104	11
α-helix	107-127	21
α-helix	148-151	4
α-helix	158-166	9
β-strand	173-174	2	12
α-helix	176-202	27
β-strand	208-209	2	11
α-helix	211-219	9
α-helix	222-227	6

Chain G: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-49	9
β-strand	56-57	2	13
α-helix	59-86	28
β-strand	91-92	2	14
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-151	4
α-helix	158-166	9
β-strand	173-174	2	14
α-helix	176-202	27
β-strand	208-209	2	13
α-helix	211-220	10
α-helix	222-227	6

Chain H: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	15
α-helix	59-86	28
β-strand	91-92	2	16
α-helix	94-104	11
α-helix	107-126	20
α-helix	148-151	4
α-helix	158-166	9
β-strand	173-174	2	16
α-helix	176-202	27
β-strand	208-209	2	15
α-helix	211-219	9
α-helix	222-227	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2B,Histone H2A	A, B, C, D, E, F, G, H	protein	208	Saccharomyces cerevisiae (strain RM11-1a)	P02293 (AlphaFold model), P04911 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>7DLX_1 Histone H2B,Histone H2A (chains A, B, C, D, E, F, G, H)
MRKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISA
REIQTAVRLILPGELAKHAVSEGTRAVTKYSSSTQASGGKGGKAGSAAKASQSRSAKAGL
TFPVGRVHRLLRRGNYAQRIGSKAAIYLTAVLEYLTAEVLELAGNAARDNKKTRIIPRHL
QLAIRNDDELNKLLGNVTIAQGGVLPNI

Primary citation

Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange. Dai, L., Xiao, X., Pan, L. et al. Cell Rep (2021) 35:109183-109183. DOI 10.1016/j.celrep.2021.109183 · PubMed

Other PDB entries of the same protein (UniProt P02293 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AE8 1.65 Å, Structure insight into histone chaperone Chz1-mediated H2A.Z recognition and replacement
4M6B 1.78 Å, Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer
4WNN 1.8 Å, SPT16-H2A-H2B FACT HISTONE Complex
5BT1 2.62 Å, histone chaperone Hif1 playing with histone H2A-H2B dimer
9C9G 2.91 Å, S.c INO80 in complex with S.c 0/80 nucleosome
9C9S 3.09 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 1
7K78 3.1 Å, antibody and nucleosome complex
9C9T 3.16 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 2
7SSA 3.2 Å, Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
9OB1 3.2 Å, S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State
4KUD 3.2 Å, Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with…
7ON1 3.35 Å, Cenp-A nucleosome in complex with Cenp-C

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