6IY3: Histone H3

Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state. Determined by electron microscopy at 3.67 Å resolution. Released 3 Apr 2019.

Method: Electron microscopy
Resolution: 3.67 Å
Organisms: Xenopus laevis, Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 11
Atoms: 17,073
Mol. weight: 260.86 kDa
Ligands: ADP
Released: 3 Apr 2019

Explore 6IY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IY3 contains 73 α-helices and 30 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	40-42	3
α-helix	45-56	12
α-helix	64-76	13
β-strand	84	1	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	81	1	1
α-helix	83-93	11
β-strand	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
α-helix	100	1
β-strand	101-102	2	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	104-123	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	97-98	2	6

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
α-helix	47-72	26
β-strand	77-78	2	9
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3

Chain H: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	30-34	5
α-helix	38-48	11
β-strand	53-54	2	9
α-helix	57-83	27
α-helix	91-101	11
α-helix	104-123	20

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	100	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	88	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	113	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	98	Xenopus laevis	P02281 (AlphaFold model)
DNA (147-mer)	J	DNA	147	Mus musculus
DNA (147-mer)	I	DNA	147	Mus musculus
Transcription regulatory protein SNF2	O	protein	679	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22082

Sequence of entity 1 (A, E), FASTA

>6IY3_1 Histone H3 (chains A, E)
KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA
SEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6IY3_2 Histone H4 (chains B, F)
AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE
HAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6IY3_3 Histone H2A (chains C, G)
KTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGN
AARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTE

Sequence of entity 4 (D, H), FASTA

>6IY3_4 Histone H2B (chains D, H)
KRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRS
TITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 5 (J), FASTA

>6IY3_5 DNA (147-MER) (chains J)
ATCTGCAACAGTCCTAACATTCACCTCTTGTGTGTTTGTGTCTGTTCGCCATCCCGTCTC
CGCTCGTCACTTATCCTTCACTTTCCAGAGGGTCCCCCCGCAGACCCCGGCGACCCTCAG
GTCGGCCGACTGCGGCACAGTTTTGAT

Sequence of entity 6 (I), FASTA

>6IY3_6 DNA (147-MER) (chains I)
ATCAAAACTGTGCCGCAGTCGGCCGACCTGAGGGTCGCCGGGGTCTGCGGGGGGACCCTC
TGGAAAGTGAAGGATAAGTGACGAGCGGAGACGGGATGGCGAACAGACACAAACACACAA
GAGGTGAATGTTAGGACTGTTGCAGAT

Sequence of entity 7 (O), FASTA

>6IY3_7 Transcription regulatory protein SNF2 (chains O)
LLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMVPKMK
DEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNHLNGI
LADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTISFKG
SPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSKLSLT
LNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGGQDKI
ELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQMLKY
RRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRVAGKF
ELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSELLRLF
NAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNEVRIL
RLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERRKKRE
SGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPDIYSR
DIGAELKREESESAAVYNG

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Li, M., Xia, X., Tian, Y. et al. Nature (2019) 567:409-413. DOI 10.1038/s41586-019-1029-2 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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