8I17: H2A-H2B recognitions by human Spt16

Structural basis for H2A-H2B recognitions by human Spt16. Determined by X-ray diffraction at 1.98 Å resolution. Released 22 Feb 2023.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 9
Atoms: 4,432
Mol. weight: 80.88 kDa
Released: 22 Feb 2023

Explore 8I17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I17 contains 35 α-helices and 18 β-strands across 9 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	17-20	4
α-helix	27-36	10
β-strand	42-43	2	1
α-helix	46-72	27
β-strand	77-78	2	2
α-helix	80-89	10
α-helix	91-97	7

Chains B and E: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	2
β-strand	55	1	3
α-helix	56-83	28
β-strand	88-89	2	1
α-helix	91-101	11
α-helix	104-123	20

Chain C: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	939-944	6
α-helix	946	1
β-strand	947	1	3
α-helix	948	1

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
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	91-97	7

Chain F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	941-944	4
α-helix	946	1
β-strand	947	1	6
α-helix	948	1

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	7
α-helix	46-72	27
β-strand	77-78	2	8
α-helix	80-89	10
α-helix	91-97	7

Chain H: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	8
β-strand	55	1	9
α-helix	56-83	28
β-strand	88-89	2	7
α-helix	91-101	11
α-helix	104-122	19

Chain I: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	946	1
β-strand	947	1	9
α-helix	948	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A type 1-B/E	A, D, G	protein	100	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	B, E, H	protein	100	Homo sapiens	P06899 (AlphaFold model)
FACT complex subunit SPT16	C, F, I	protein	42	Homo sapiens	Q9Y5B9 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>8I17_1 Histone H2A type 1-B/E (chains A, D, G)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQ

Sequence of entity 2 (B, E, H), FASTA

>8I17_2 Histone H2B type 1-J (chains B, E, H)
SKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNK
RSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 3 (C, F, I), FASTA

>8I17_3 FACT complex subunit SPT16 (chains C, F, I)
GPEPEGEGSDAEEGDSESEIEDETFNPSEDDYEEEEEDSDED

Primary citation

Structural basis for H2A-H2B recognitions by human Spt16. Li, Y., Huang, H. Biochem Biophys Res Commun (2023) 651:85-91. DOI 10.1016/j.bbrc.2023.02.016 · PubMed

Other PDB entries of the same protein (UniProt P04908 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VZ4 1.89 Å, Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA…
6ACL 1.92 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
5Y0D 1.99 Å, Crystal Structure of the human nucleosome containing the H2B E76K mutant
6IPU 1.99 Å, Human nucleosome core particle containing 145 bp of DNA
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5Y0C 2.09 Å, Crystal Structure of the human nucleosome at 2.09 angstrom resolution
8Q3E 2.17 Å, High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide
5X7X 2.18 Å, The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution
5AV6 2.2 Å, human nucleosome core particle
5AV8 2.2 Å, human nucleosome core particle
5AV9 2.2 Å, human nucleosome core particle

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