6FTX: Chromatin remodelling enzyme Chd1

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. Determined by electron microscopy at 4.5 Å resolution. Released 8 Aug 2018.

Method
Electron microscopy
Resolution
4.5 Å
Organisms
Petromyzon marinus, Xenopus laevis, Xenopus tropicalis
Chains
13
Atoms
21,049
Mol. weight
320.89 kDa
Ligands
ADP, BEF
Released
8 Aug 2018

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

Secondary structure: helices and β-sheets

6FTX contains 75 α-helices and 52 β-strands across 11 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, 1 β-strand

ElementResiduesLengthSheet
α-helix41-422
α-helix47-5610
α-helix64-7815
α-helix86-11328
β-strand118-11921
α-helix121-13111
Chain B: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix26-283
α-helix31-4111
β-strand45-4621
α-helix50-7526
α-helix83-9311
β-strand97-9822
Chain C: 5 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix18-214
α-helix27-3610
α-helix46-7227
β-strand77-7823
α-helix80-8910
α-helix92-965
β-strand101-10224
Chain D: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix35-4511
β-strand50-5123
α-helix55-7824
α-helix88-9811
α-helix101-12020
Chain E: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix49-568
α-helix66-7813
α-helix86-11328
β-strand118-11925
α-helix123-1319
Chain F: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix31-4111
β-strand45-4625
α-helix48-7528
α-helix81-822
α-helix83-9210
β-strand97-9824
Chain G: 5 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix17-204
α-helix27-337
β-strand4316
α-helix47-7226
α-helix80-8910
α-helix91-977
β-strand101-10222
Chain H: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix35-4511
α-helix53-8028
β-strand8616
α-helix90-989
α-helix101-12020

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Histone H3Aprotein97Petromyzon marinusS4RAZ3 (AlphaFold model)
Histone H4B, Fprotein103Xenopus laevisP62799 (AlphaFold model)
Histone H2A type 1C, Gprotein130Xenopus laevisP06897 (AlphaFold model)
Histone H2BD, Hprotein126Xenopus tropicalisQ28D68 (AlphaFold model)
Histone H3.3CEprotein110Xenopus laevisP02302
DNA (159-mer)IDNA159synthetic construct
DNA (160-mer)JDNA160synthetic construct
Polyubiquitin-BN, Oprotein76Homo sapiensP0CG47
Chromatin-remodeling ATPaseWprotein878Saccharomyces cerevisiaeP32657
Sequence of entity 1 (A), FASTA
>6FTX_1 Histone H3 (chains A)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B, F), FASTA
>6FTX_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6FTX_3 Histone H2A type 1 (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESAKSAKSK
Sequence of entity 4 (D, H), FASTA
>6FTX_4 Histone H2B (chains D, H)
MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (E), FASTA
>6FTX_5 Histone H3.3C (chains E)
AAAAAAAAAAAAAHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQ
SSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 6 (I), FASTA
>6FTX_6 DNA (159-MER) (chains I)
ATACGCGGCCGCCCATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTC
TAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTAC
TCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT
Sequence of entity 7 (J), FASTA
>6FTX_7 DNA (160-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTTCGGCACCGGGATTCTGATGGGCGGCCGCGTAT
Sequence of entity 8 (N, O), FASTA
>6FTX_8 Polyubiquitin-B (chains N, O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 9 (W), FASTA
>6FTX_9 Chromatin-remodeling ATPase (chains W)
DFHGIDIVINHRLKTSKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRL
DNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGT
SQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFE
KLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFAR
RQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKT
MKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITG
TPLQNNIKELAALVNFLMPGRFNQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTE
RILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEER
VLQKFMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKG
INFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNP
QADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEYDMDSIGESEVRALY
KAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLE
KHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVED
LKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIR
DDPFLGITDKIFLKKVPGAIHLGRRVDYLLSFLRGGLN

Ligands and cofactors

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

Primary citation

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. Sundaramoorthy, R., Hughes, A.L., El-Mkami, H. et al. Elife (2018) 7. DOI 10.7554/eLife.35720 · PubMed

Other PDB entries of the same protein (UniProt S4RAZ3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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