6TDA: SWI/SNF chromatin remodeler RSC
Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome. Determined by electron microscopy at 15.0 Å resolution. Released 18 Mar 2020.
- Method
- Electron microscopy
- Resolution
- 15.0 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 23
- Atoms
- 42,577
- Mol. weight
- 1054.13 kDa
- Ligands
- ZN
- Released
- 18 Mar 2020
Explore 6TDA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6TDA contains 231 α-helices and 150 β-strands across 21 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 121-131 | 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 | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 5 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 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-43 | 9 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| 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: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
13 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 H3.2 | A, E | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 129 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA-I | I | DNA | 237 | synthetic construct | |
| DNA-J | J | DNA | 237 | synthetic construct | |
| Chromatin structure-remodeling complex subunit SFH1 | K | protein | 426 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q06168 |
| Chromatin structure-remodeling complex protein RSC8 | L | protein | 1114 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P43609 |
| Chromatin structure-remodeling complex subunit RSC7 | M | protein | 435 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32832 |
| Chromatin structure-remodeling complex subunit RSC9 | N | protein | 581 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q03124 |
| Chromatin structure-remodeling complex protein RSC6 | O | protein | 483 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25632 |
| Chromatin structure-remodeling complex protein RSC58 | P | protein | 502 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q07979 |
7 more molecules are not listed.
Sequence of entity 1 (A, E), FASTA
>6TDA_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6TDA_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6TDA_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6TDA_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (I), FASTA
>6TDA_5 DNA-I (chains I)
CCTACGGACCGGATATCTTCCCTGTGTATGGGTTTCCATCAGAATCCCGGTGCCGAGGCC
GCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGC
GTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCG
ATTTAACTCTTTTCGTCGGTTTTTTTCGCCTTTAAAACTAGGCGGGCTGGGTAATGA
Sequence of entity 6 (J), FASTA
>6TDA_6 DNA-J (chains J)
TCATTACCCAGCCCGCCTAGTTTTAAAGGCGAAAAAAACCGACGAAAAGAGTTAAATCGA
TGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCG
GGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGC
CTCGGCACCGGGATTCTGATGGAAACCCATACACAGGGAAGATATCCGGTCCGTAGG
Sequence of entity 7 (K), FASTA
>6TDA_7 Chromatin structure-remodeling complex subunit SFH1 (chains K)
MSHQNQLIPQAYISNFHNRLTNEDDGIPIFTMAQQTRQHKRAKVVNYAEYDNDLFDEFNM
NGSNFNNADTHYKDNAVSHENTPALTNGVTMDGSEYNVLENMNGADSIISNNKYDAGSNM
VVESLSGLNSNNNASNGPSNKAQAQDIGNAVLPDLQDQHHNPFNILRYPKIRDTFINGKV
VSPYRLNTDQETKANANSGEAIMIPITLDIEHMGHTIKDQFLWNYNDDSISPEEFASIYC
KDLDMTSATLQTQIANIIKEQLKDLENIAATEIMSDLHVIINLTCNLQDRFFEDNFQWNL
NDKSLTPERFATSIVQDLGLTREFIPLISQSLHETILKIKKDWVDGHLIQDHVPNDAAFG
YLSGIRLDIDELGSNWCPRVEILTKEEIQKREIEKERNLRRLKRETDRLSRRGRRRLDDL
ETTMRM
Sequence of entity 8 (L), FASTA
>6TDA_8 Chromatin structure-remodeling complex protein RSC8 (chains L)
MSDTEKDKDVPMVDSHEATEEPPTTSTNTPSFPHLAQEQAKEESATLGAEVAHKKINYEQ
EAQKLEEKALRFLAKQTHPVIIPSFASWFDISKIHEIEKRSNPDFFNDSSRFKTPKAYKD
TRNFIINTYRLSPYEYLTITAVRRNVAMDVASIVKIHAFLEKWGLINYQIDPRTKPSLIG
PSFTGHFQVVLDTPQGLKPFLPENVIKQEVEGGDGAEPQVKKEFPVNLTIKKNVYDSAQD
FNALQDESRNSRQIHKVYICHTCGNESINVRYHNLRARDTNLCSRCFQEGHFGANFQSSD
FIRLENNGNSVKKNWSDQEMLLLLEGIEMYEDQWEKIADHVGGHKRVEDCIEKFLSLPIE
DNYIREVVGSTLNGKGGDSRDGSVSGSKLMECVNDAVQTLLQGDDKLGKVSDKSREISEK
YIEESQAIIQELVKLTMEKLESKFTKLCDLETQLEMEKLKYVKESEKMLNDRLSLSKQIL
DLNKSLEELNVSKKLVLISEQVDSGIQLVEKDQEGDDEDGNTATGHGVKRVGKEGEEVGE
GDSIAKLQPQVYKPWSLMSDTEKDKDVPMVDSHEATEEPPTTSTNTPSFPHLAQEQAKEE
SATLGAEVAHKKINYEQEAQKLEEKALRFLAKQTHPVIIPSFASWFDISKIHEIEKRSNP
DFFNDSSRFKTPKAYKDTRNFIINTYRLSPYEYLTITAVRRNVAMDVASIVKIHAFLEKW
GLINYQIDPRTKPSLIGPSFTGHFQVVLDTPQGLKPFLPENVIKQEVEGGDGAEPQVKKE
FPVNLTIKKNVYDSAQDFNALQDESRNSRQIHKVYICHTCGNESINVRYHNLRARDTNLC
SRCFQEGHFGANFQSSDFIRLENNGNSVKKNWSDQEMLLLLEGIEMYEDQWEKIADHVGG
HKRVEDCIEKFLSLPIEDNYIREVVGSTLNGKGGDSRDGSVSGSKLMECVNDAVQTLLQG
DDKLGKVSDKSREISEKYIEESQAIIQELVKLTMEKLESKFTKLCDLETQLEMEKLKYVK
ESEKMLNDRLSLSKQILDLNKSLEELNVSKKLVLISEQVDSGIQLVEKDQEGDDEDGNTA
TGHGVKRVGKEGEEVGEGDSIAKLQPQVYKPWSL
Sequence of entity 9 (M), FASTA
>6TDA_9 Chromatin structure-remodeling complex subunit RSC7 (chains M)
MSDSEGGLASEVEHEKRSRSTSNRPNYAIDTEDLDIDENDENEDDDYREEEANEGVNEEE
ISDEEEQINKSGRNKRRHVDEEEDLSEDKGVTRSRNRSKFKKPVFPGIDDAEENLNPLKV
VNEEYVLPDDPEGETKITADGDLLGGREFLVRTFTLTEKGNRKFMLATEPARIVGFRDSY
LFFQTHPNLYKFILNQTQKNDLIDRGVLPYSYRNRQIALVTARGVFKEFGAKIIRGGKHI
TDDYYASELRTKGNVIEGKLAGDPIDKSARALETMMYPASENGINPAKNQVEFFEHRPHG
HMSNSNIIASGSKLSSTNWLYQHSAACSRFNSDLFYDRVKVLLVDQQGLRDAYTNILHIP
ESTQSTTVLGWRRSKNDSPSDTSIVYETVIHDNDLNKPKTGLSEIPKEIYEDVVDEDVLR
AITEQQNFEKCNEYI
Sequence of entity 10 (N), FASTA
>6TDA_10 Chromatin structure-remodeling complex subunit RSC9 (chains N)
MNSLASNTPLNGTPVSEAPATSSEPVNMFETMVANPIKVSRLQSNGVLTGPAANTKSIHY
SLANFNVFQSLPKETARGVDDLTRMEMALLSGIPEEIKWSLKKYLTYSNKAPYMISLRTL
PDLLPLFKTFILPLERIVEGLNKSSICDSKAMDSLQMGLNALLILRNLAQDTDSVQILVK
DREIKSFILFILKKFQCVATGDNKWQLYEGNATFFNELTHYTLDLMEAISSYIAPAMKDD
HYFQTLVSILNYTKDRYMVISILRSLSRLLVRSKANEESAADNLDHKTLSLIVSFLLLEC
DSELIIASLDFLYQYILPGSQRITELFKSKECSLILEATLPNLLSYNIATPDYHLLQKHK
IRLIKRLKPPAPKEPPNLSEDLFQQLFKLNEPLRSTAWLRCCFEPVQEAEFTQISLWRSY
ESKFGQPVRESGRKLLPAVEFIKNVSNAFNNAAAIVITDPVTGKKRFVIKGIQPRFKALG
IADGERESQVPISALKSKFLNDSKEITPARQNSIPEVKFPQELSDVSKVACTFLCLLSND
TDDGAGSAFCQRIRPLVLHKLADIPPLTLALSEYMENTSGL
Sequence of entity 11 (O), FASTA
>6TDA_11 Chromatin structure-remodeling complex protein RSC6 (chains O)
MVTQTNPVPVTYPTDAYIPTYLPDDKVSNLADLKKLIEMDSRLDLYLTRRRLDTSINLPT
NTKTKDHPPNKEMLRIYVYNTTESSPRSDSGTPADSGKTTWTLRIEGKLLHESANGKHPF
SEFLEGVAVDFKRLKPLGMGKKRKRDSSLSLPLNLQQPEYNDQDSTMGDNDNGEDEDSAE
AESREEIVDALEWNYDENNVVEFDGIDIKRQGKDNLRCSITIQLRGVDGGKVQYSPNLAT
LIGMQTGSVNDAVYSIYKYILINNLFVTEQTEAQDGSNDAEDSSNENNNKNGAGDDDGVE
GSTPKDKPELGEVKLDSLLQKVLDTNAAHLPLMNVVQTVNKLVSPLPPIILDYTIDLSKD
TTYGATTLDVDVSHILHQPQPQPNLQKEEETDAEDTAKLREITKLALQLNSSAQKYQFFH
ELSLHPRETLTHYLWSSKQNELVLQGDQYFNEDAARTSDIYSNNNNDRSLMGNISLLYSQ
GRL
Sequence of entity 12 (P), FASTA
>6TDA_12 Chromatin structure-remodeling complex protein RSC58 (chains P)
MTESVGGNKLVDFLVNVQSILNAASVKCHVVDESFPAKFFEKNPDKIYESYCKFIKNRSN
SEGLIRNEDKLVLTTINKRFENGEYEPIQGGFYKLYHDIKLVCTILIHFYPQGTRNYQLV
DKFYKFSSELLLRECCRIGIALTQTNNIKSRSGKLLSGNEMDEYDDDDATELDKIISYDF
IKISMNYTVPISQTYQIRTKDMDLFSSIISKSNLDKRPHELPNTNFKINNVLPQTDIENE
APRLGFVGANTSNIPDPTLPPTEMMTRFLHPNWYALPTTVWLKYGNYNSWAPSFNENGTV
VDSTTRGLIWLERIGYMDLYEKNEKKVKQEELLNTNEEGINRKQNDENNKNVDGKSNGVQ
DDGGDNDNDATIASANSESTENKEQFIIKLQNLYNWTPSNYIGDDEIENFRNGTPDKLVS
DSLLKLKRLRKERILNKVLKPTTEERELYFKVKRILKEVILAKKVSKVPINNVRAFPVLQ
TNYNGSIPVVRAQPGRKRKHKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome. Wagner, F.R., Dienemann, C., Wang, H. et al. Nature (2020) 579:448-451. DOI 10.1038/s41586-020-2088-0 · 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
Browse structure collections
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