8KCC: Probable histone H2A.7

Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2. Determined by electron microscopy at 3.1 Å resolution. Released 26 Jun 2024.

Method
Electron microscopy
Resolution
3.1 Å
Organisms
Arabidopsis thaliana, synthetic construct
Chains
11
Atoms
16,271
Mol. weight
309.22 kDa
Ligands
BEF, ADP
Released
26 Jun 2024

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

Secondary structure: helices and β-sheets

8KCC contains 64 α-helices and 40 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, 3 β-strands

ElementResiduesLengthSheet
α-helix26-305
α-helix36-4611
β-strand51-5221
α-helix55-8127
β-strand86-8722
α-helix89-9810
α-helix100-1056
β-strand109-11023
Chain B: 5 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix26-294
α-helix36-4611
β-strand51-5224
α-helix56-8126
β-strand86-8725
α-helix89-9810
α-helix100-1056
β-strand110-11126
Chains C and D: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix58-6811
β-strand73-7425
α-helix76-10328
β-strand108-10924
α-helix111-12111
α-helix125-14319
Chains E and F: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix43-5715
α-helix64-7815
β-strand83-8427
α-helix86-11328
β-strand118-11928
α-helix121-13111
Chain G: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix26-283
α-helix31-4111
β-strand45-4628
α-helix50-7526
β-strand80-8127
α-helix83-9210
β-strand97-9826
Chain H: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix21-244
α-helix31-4111
β-strand45-46210
α-helix49-7527
β-strand80-8129
α-helix83-9210
β-strand96-9723
Chain K: 30 helices, 20 β-strands
ElementResiduesLengthSheet
α-helix184-19310
α-helix204-21916
β-strand223111
β-strand224-225212
β-strand226113
α-helix233-24614
β-strand253-256414
α-helix259-27113
β-strand278-281414
α-helix285-29511
β-strand306-309414
α-helix311-3177
α-helix318-3225
β-strand327-333714
α-helix335-3384
α-helix344-3518
β-strand354-356314
β-strand358111
β-strand359-360214
β-strand361113
α-helix371-3799
α-helix387-3937
α-helix411-42313
β-strand428-429212
α-helix441-4422
β-strand443-451915
α-helix452-4532
α-helix454-46411
α-helix468-4714
α-helix489-4979
α-helix500-5089
α-helix513-5153
α-helix516-5227
α-helix526-53914
β-strand543-547515
α-helix550-56314
β-strand567-570415
α-helix576-58611
β-strand595-599515
β-strand614-617415
α-helix624-6318
α-helix6421
β-strand643-651915
α-helix655-67016
α-helix706-7105
α-helix712-7143
α-helix715-7228
β-strand744-745215
β-strand748-750315
α-helix760-7634

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Probable histone H2A.7A, Bprotein150Arabidopsis thalianaQ9FJE8 (AlphaFold model)
Histone H2B.10C, Dprotein145Arabidopsis thalianaQ9FFC0 (AlphaFold model)
Histone H3.1E, Fprotein136Arabidopsis thalianaP59226 (AlphaFold model)
Histone H4G, Hprotein103Arabidopsis thalianaP59259 (AlphaFold model)
DNA (170-mer)IDNA170synthetic construct
DNA (170-mer)JDNA170synthetic construct
ATP-dependent DNA helicase DDM1Kprotein764Arabidopsis thalianaQ9XFH4
Sequence of entity 1 (A, B), FASTA
>8KCC_1 Probable histone H2A.7 (chains A, B)
MESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVY
MAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGVLPN
INSVLLPKKSATKPAEEKATKSPVKSPKKA
Sequence of entity 2 (C, D), FASTA
>8KCC_2 Histone H2B.10 (chains C, D)
MAKADKKPAEKKPAEKTPAAEPAAAAEKKPKAGKKLPKEPAGAGDKKKKRSKKNVETYKI
YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAGESSKLARYNKKPTITSREIQTAVR
LVLPGELAKHAVSEGTKAVTKFTSS
Sequence of entity 3 (E, F), FASTA
>8KCC_3 Histone H3.1 (chains E, F)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 4 (G, H), FASTA
>8KCC_4 Histone H4 (chains G, H)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (I), FASTA
>8KCC_5 DNA (170-MER) (chains I)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCACATATATACATCCTGTTCCAGTGCCGGTGTCGCGAT
Sequence of entity 6 (J), FASTA
>8KCC_6 DNA (170-MER) (chains J)
ATCGCGACACCGGCACTGGAACAGGATGTATATATGTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT
Sequence of entity 7 (K), FASTA
>8KCC_7 ATP-dependent DNA helicase DDM1 (chains K)
MVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKNGDS
SLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFLLEK
MEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETINSDL
TEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIGF
LSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMPKTV
GPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNKLLL
TGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVVSKL
HGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAIRGQ
GWKGKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLFANN
HKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLST
RAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLK
RAYSKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDADLDR
LLDRSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS

Ligands and cofactors

IDNameFormulaCopies
BEFBeryllium trifluoride ionBe F31
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21

Primary citation

Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures. Zhang, H., Gu, Z., Zeng, Y. et al. Structure (2024) 32:1222-1230.e4. DOI 10.1016/j.str.2024.05.013 · PubMed

Other PDB entries of the same protein (UniProt Q9FJE8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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