5GSU: Histone H3.1

Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B. Determined by X-ray diffraction at 3.1 Å resolution. Released 15 Feb 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,086
Mol. weight: 200.57 kDa
Ligands: MN
Released: 15 Feb 2017

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

Secondary structure: helices and β-sheets

5GSU contains 40 α-helices and 20 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	5

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	29-37	9
β-strand	44-45	2	7
α-helix	48-74	27
β-strand	79-80	2	8
α-helix	82-90	9
α-helix	93-98	6
β-strand	102-104	3	6
α-helix	115-117	3

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	8
α-helix	54-81	28
β-strand	86-87	2	7
α-helix	89-99	11
α-helix	101	1
α-helix	104-122	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	3
α-helix	86-113	28
β-strand	118-119	2	4
α-helix	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	4
α-helix	50-75	26
β-strand	80-81	2	3
α-helix	83-91	9
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	29-37	9
β-strand	44-45	2	9
α-helix	49-74	26
β-strand	79-80	2	10
α-helix	82-90	9
α-helix	93-98	6
β-strand	102-104	3	5
α-helix	115-117	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	10
α-helix	54-81	28
β-strand	86-87	2	9
α-helix	89-99	11
α-helix	102-122	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	135	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-A	C, G	protein	130	Homo sapiens	Q96QV6 (AlphaFold model)
Histone H2B type 1-A	D, H	protein	126	Homo sapiens	Q96A08 (AlphaFold model)
DNA (146-mer)	I, J	DNA	146	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>5GSU_1 Histone H3.1 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5GSU_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5GSU_3 Histone H2A type 1-A (chains C, G)
SGRGKQGGKARAKSKSRSSRAGLQFPVGRIHRLLRKGNYAERIGAGAPVYLAAVLEYLTA
EILELAGNASRDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT
ESHHHKAQSK

Sequence of entity 4 (D, H), FASTA

>5GSU_4 Histone H2B type 1-A (chains D, H)
PEVSSKGATISKKGFKKAVVKTQKKEGKKRKRTRKESYSIYIYKVLKQVHPDTGISSKAM
SIMNSFVTDIFERIASEASRLAHYSKRSTISSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 5 (I, J), FASTA

>5GSU_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	15

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b. Padavattan, S., Thiruselvam, V., Shinagawa, T. et al. Biophys Chem (2017) 221:41-48. DOI 10.1016/j.bpc.2016.11.013 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

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