6KBB: Histone H2A type 1-D

Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition. Determined by X-ray diffraction at 2.37 Å resolution. Released 29 Jan 2020.

Method: X-ray diffraction
Resolution: 2.37 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 6
Atoms: 3,067
Mol. weight: 62.11 kDa
Released: 29 Jan 2020

Explore 6KBB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KBB contains 24 α-helices and 12 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6

Chains B and D: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	32-36	5
α-helix	38-48	11
β-strand	53-54	2	5
β-strand	55	1	6
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	104-122	19

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	1
α-helix	46-72	27
β-strand	77-78	2	2
α-helix	80-88	9
α-helix	91-97	7

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	28	1	6

Chain F: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-19	4
α-helix	23-25	3
α-helix	27	1
β-strand	28	1	3
α-helix	29	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A type 1-D	A, C	protein	96	Homo sapiens	P20671 (AlphaFold model)
Histone H2B type 2-E	B, D	protein	104	Homo sapiens	Q16778 (AlphaFold model)
SWR1-complex protein 5	E, F	protein	81	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38326 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6KBB_1 Histone H2A type 1-D (chains A, C)
GSKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGG

Sequence of entity 2 (B, D), FASTA

>6KBB_2 Histone H2B type 2-E (chains B, D)
MGSMGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLA
HYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Sequence of entity 3 (E, F), FASTA

>6KBB_3 SWR1-complex protein 5 (chains E, F)
GSMPEVETKIIPNEKEDEDEDGYIEEEDEDFQPEKDKLGGGSDDSDASDGGDDYDDGVNR
DKGRNKVDYSRIESESGGLIK

Primary citation

Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing. Huang, Y., Sun, L., Pierrakeas, L. et al. Proc Natl Acad Sci U S A (2020) 117:3543-3550. DOI 10.1073/pnas.1914313117 · PubMed

Other PDB entries of the same protein (UniProt P20671 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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9W6Q 3.43 Å, Cryo-EM structure of a stacked human nucleosome core particle trimer assembled with DNA…
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9W6E 3.7 Å, Cryo-EM structure of a stacked human nucleosome core particle dimer assembled with DNA…
9W6K 3.71 Å, Cryo-EM structure of a stacked human nucleosome core particle dimer (type 1&2, bottom…
9W6G 4.02 Å, Cryo-EM structure of a stacked human nucleosome core particle tetramer assembled with…
9W6O 4.08 Å, Cryo-EM structure of a stacked human nucleosome core particle dimer (type 6, top NCP)…
8YJM 4.15 Å, Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a…
8YJF 4.4 Å, Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an…

Browse structure collections

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