6KW4: The ClassB RSC-Nucleosome Complex
The ClassB RSC-Nucleosome Complex. Determined by electron microscopy at 7.55 Å resolution. Released 13 Nov 2019.
- Method
- Electron microscopy
- Resolution
- 7.55 Å
- Organisms
- Xenopus laevis, Homo sapiens, Saccharomyces cerevisiae S288C
- Chains
- 28
- Atoms
- 45,924
- Mol. weight
- 1598.36 kDa
- Ligands
- ZN
- Released
- 13 Nov 2019
Explore 6KW4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6KW4 contains 245 α-helices and 158 β-strands across 26 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: 19 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-23 | 14 | |
| α-helix | 44-46 | 3 | |
| α-helix | 49-57 | 9 | |
| α-helix | 76-81 | 6 | |
| α-helix | 89-109 | 21 | |
| α-helix | 115-132 | 18 | |
| α-helix | 173-179 | 7 | |
| β-strand | 186 | 1 | 38 |
| β-strand | 188-189 | 2 | 39 |
| β-strand | 192-197 | 6 | 32 |
| β-strand | 204-205 | 2 | 32 |
| β-strand | 227-231 | 5 | 32 |
| α-helix | 232-234 | 3 | |
| α-helix | 238-242 | 5 | |
| β-strand | 243 | 1 | 40 |
| α-helix | 254-256 | 3 | |
| α-helix | 274-277 | 4 | |
| β-strand | 280-283 | 4 | 33 |
| β-strand | 294-295 | 2 | 33 |
| α-helix | 303-311 | 9 | |
| α-helix | 391-394 | 4 | |
| α-helix | 407-410 | 4 | |
| α-helix | 417-434 | 18 | |
| α-helix | 441-442 | 2 | |
| α-helix | 443-458 | 16 | |
| α-helix | 459-463 | 5 | |
| β-strand | 475 | 1 | 41 |
| β-strand | 478-479 | 2 | 42 |
| β-strand | 480 | 1 | 43 |
| α-helix | 488-489 | 2 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 48-50 | 3 | |
| α-helix | 53-75 | 23 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 97 | 1 | 3 |
Chain C: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 195 | 1 | 44 |
| β-strand | 198-200 | 3 | 45 |
| α-helix | 205-225 | 21 | |
Chain D: 18 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 69-75 | 7 | |
| α-helix | 78-80 | 3 | |
| α-helix | 96-101 | 6 | |
| α-helix | 103-105 | 3 | |
| α-helix | 115-129 | 15 | |
| α-helix | 139-142 | 4 | |
| β-strand | 149 | 1 | 30 |
| α-helix | 150-162 | 13 | |
| β-strand | 179-180 | 2 | 23 |
| α-helix | 181-183 | 3 | |
| β-strand | 189-192 | 4 | 25 |
| β-strand | 193 | 1 | 31 |
| β-strand | 196 | 1 | 31 |
| β-strand | 199 | 1 | 25 |
| α-helix | 224-226 | 3 | |
| α-helix | 232-233 | 2 | |
| α-helix | 242-244 | 3 | |
| α-helix | 317-329 | 13 | |
| α-helix | 336-341 | 6 | |
| α-helix | 347-354 | 8 | |
| α-helix | 357-360 | 4 | |
| α-helix | 361-367 | 7 | |
| α-helix | 390-396 | 7 | |
| α-helix | 416-484 | 69 | |
Chain E: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-39 | 19 | |
| α-helix | 47-53 | 7 | |
| α-helix | 55-72 | 18 | |
Chain f: 22 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-12 | 5 | 14 |
| β-strand | 16-21 | 6 | 14 |
| β-strand | 29-32 | 4 | 14 |
| β-strand | 34-38 | 5 | 15 |
| β-strand | 46-48 | 3 | 15 |
| α-helix | 52-59 | 8 | |
| β-strand | 66-69 | 4 | 15 |
| β-strand | 71 | 1 | 16 |
| β-strand | 77 | 1 | 16 |
| α-helix | 80-88 | 9 | |
| α-helix | 89-94 | 6 | |
| β-strand | 104-108 | 5 | 14 |
| α-helix | 116-127 | 12 | |
| β-strand | 135-140 | 6 | 14 |
| α-helix | 141-148 | 8 | |
| β-strand | 154-159 | 6 | 17 |
| β-strand | 164-170 | 7 | 17 |
| β-strand | 173-174 | 2 | 17 |
| α-helix | 176-178 | 3 | |
| β-strand | 180-181 | 2 | 17 |
| α-helix | 186-196 | 11 | |
| α-helix | 217-226 | 10 | |
| α-helix | 228-230 | 3 | |
| α-helix | 231-235 | 5 | |
| β-strand | 237 | 1 | 18 |
| α-helix | 243-261 | 19 | |
| β-strand | 288-292 | 5 | 19 |
| β-strand | 297-301 | 5 | 19 |
| α-helix | 303-311 | 9 | |
| α-helix | 316-318 | 3 | |
| α-helix | 329-341 | 13 | |
| α-helix | 381-389 | 9 | |
| β-strand | 392-395 | 4 | 17 |
| α-helix | 398-400 | 3 | |
| β-strand | 402 | 1 | 18 |
| α-helix | 404-413 | 10 | |
| α-helix | 420-421 | 2 | |
| β-strand | 423-425 | 3 | 17 |
| α-helix | 429-433 | 5 | |
| α-helix | 435-444 | 10 | |
| α-helix | 449-451 | 3 | |
| β-strand | 454-456 | 3 | 14 |
| α-helix | 457-464 | 8 | |
Chain F: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 320-339 | 20 | |
| α-helix | 340-345 | 6 | |
| β-strand | 359-360 | 2 | 23 |
| α-helix | 361-363 | 3 | |
| β-strand | 368-372 | 5 | 24 |
| β-strand | 384-389 | 6 | 24 |
| α-helix | 409-411 | 3 | |
| α-helix | 417-430 | 14 | |
Chain g: 18 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| β-strand | 10-14 | 5 | 22 |
| β-strand | 18-23 | 6 | 22 |
| β-strand | 35-38 | 4 | 22 |
| β-strand | 41-45 | 5 | 52 |
| β-strand | 51-54 | 4 | 52 |
| β-strand | 62-65 | 4 | 52 |
| β-strand | 68-69 | 2 | 53 |
| β-strand | 72-73 | 2 | 53 |
| α-helix | 76-97 | 22 | |
| β-strand | 110-115 | 6 | 22 |
| α-helix | 121-133 | 13 | |
| β-strand | 139-144 | 6 | 22 |
| α-helix | 145-150 | 6 | |
| β-strand | 159-164 | 6 | 54 |
| β-strand | 169-175 | 7 | 54 |
| β-strand | 178-179 | 2 | 54 |
| β-strand | 185-187 | 3 | 54 |
| α-helix | 191-201 | 11 | |
| α-helix | 207-214 | 8 | |
| β-strand | 220 | 1 | 55 |
| β-strand | 282-285 | 4 | 56 |
| β-strand | 291-294 | 4 | 56 |
| α-helix | 296-299 | 4 | |
| α-helix | 303-317 | 15 | |
| α-helix | 323-330 | 8 | |
| β-strand | 333-336 | 4 | 54 |
| α-helix | 339-341 | 3 | |
| β-strand | 343 | 1 | 55 |
| α-helix | 345-356 | 12 | |
| α-helix | 363-372 | 10 | |
| α-helix | 396-399 | 4 | |
| β-strand | 400 | 1 | 19 |
| β-strand | 409 | 1 | 54 |
| α-helix | 410-412 | 3 | |
| α-helix | 417-421 | 5 | |
| α-helix | 428-438 | 11 | |
| β-strand | 449 | 1 | 22 |
| α-helix | 451-456 | 6 | |
| α-helix | 458-464 | 7 | |
18 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 | N, Q | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, R | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | O, S | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| DNA 167 | U | DNA | 167 | Homo sapiens | |
| DNA 167 | W | DNA | 167 | Saccharomyces cerevisiae S288C | |
| Actin-related protein 7 | f | protein | 477 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12406 (AlphaFold model) |
| Regulator of Ty1 transposition protein 102 | h | protein | 157 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53330 |
| Chromatin structure-remodeling complex subunit RSC7 | F | protein | 435 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32832 |
| Chromatin structure-remodeling complex protein RSC8 | D, H | protein | 557 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P43609 |
| Chromatin structure-remodeling complex subunit RSC9 | M | protein | 581 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q03124 |
| Chromatin structure-remodeling complex protein RSC6 | I | protein | 483 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25632 |
| Chromatin structure-remodeling complex subunit SFH1 | G | protein | 426 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q06168 |
9 more molecules are not listed.
Sequence of entity 1 (N, Q), FASTA
>6KW4_1 Histone H3.2 (chains N, Q)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, R), FASTA
>6KW4_2 Histone H4 (chains B, R)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (O, S), FASTA
>6KW4_3 Histone H2A (chains O, S)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (U), FASTA
>6KW4_4 DNA 167 (chains U)
GATGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGAAGCTTGTCGAGAAGTACTAG
Sequence of entity 5 (W), FASTA
>6KW4_5 DNA 167 (chains W)
CTAGTACTTCTCGACAAGCTTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCATC
Sequence of entity 6 (f), FASTA
>6KW4_6 Actin-related protein 7 (chains f)
MTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAAE
KRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAIL
ERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAVV
RSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVSE
KDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTLT
LDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLGT
SHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQYK
LTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATN
Sequence of entity 7 (h), FASTA
>6KW4_7 Regulator of Ty1 transposition protein 102 (chains h)
MDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRY
KTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEA
LSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN
Sequence of entity 8 (F), FASTA
>6KW4_8 Chromatin structure-remodeling complex subunit RSC7 (chains F)
MSDSEGGLASEVEHEKRSRSTSNRPNYAIDTEDLDIDENDENEDDDYREEEANEGVNEEE
ISDEEEQINKSGRNKRRHVDEEEDLSEDKGVTRSRNRSKFKKPVFPGIDDAEENLNPLKV
VNEEYVLPDDPEGETKITADGDLLGGREFLVRTFTLTEKGNRKFMLATEPARIVGFRDSY
LFFQTHPNLYKFILNQTQKNDLIDRGVLPYSYRNRQIALVTARGVFKEFGAKIIRGGKHI
TDDYYASELRTKGNVIEGKLAGDPIDKSARALETMMYPASENGINPAKNQVEFFEHRPHG
HMSNSNIIASGSKLSSTNWLYQHSAACSRFNSDLFYDRVKVLLVDQQGLRDAYTNILHIP
ESTQSTTVLGWRRSKNDSPSDTSIVYETVIHDNDLNKPKTGLSEIPKEIYEDVVDEDVLR
AITEQQNFEKCNEYI
Sequence of entity 9 (D, H), FASTA
>6KW4_9 Chromatin structure-remodeling complex protein RSC8 (chains D, H)
MSDTEKDKDVPMVDSHEATEEPPTTSTNTPSFPHLAQEQAKEESATLGAEVAHKKINYEQ
EAQKLEEKALRFLAKQTHPVIIPSFASWFDISKIHEIEKRSNPDFFNDSSRFKTPKAYKD
TRNFIINTYRLSPYEYLTITAVRRNVAMDVASIVKIHAFLEKWGLINYQIDPRTKPSLIG
PSFTGHFQVVLDTPQGLKPFLPENVIKQEVEGGDGAEPQVKKEFPVNLTIKKNVYDSAQD
FNALQDESRNSRQIHKVYICHTCGNESINVRYHNLRARDTNLCSRCFQEGHFGANFQSSD
FIRLENNGNSVKKNWSDQEMLLLLEGIEMYEDQWEKIADHVGGHKRVEDCIEKFLSLPIE
DNYIREVVGSTLNGKGGDSRDGSVSGSKLMECVNDAVQTLLQGDDKLGKVSDKSREISEK
YIEESQAIIQELVKLTMEKLESKFTKLCDLETQLEMEKLKYVKESEKMLNDRLSLSKQIL
DLNKSLEELNVSKKLVLISEQVDSGIQLVEKDQEGDDEDGNTATGHGVKRVGKEGEEVGE
GDSIAKLQPQVYKPWSL
Sequence of entity 10 (M), FASTA
>6KW4_10 Chromatin structure-remodeling complex subunit RSC9 (chains M)
MNSLASNTPLNGTPVSEAPATSSEPVNMFETMVANPIKVSRLQSNGVLTGPAANTKSIHY
SLANFNVFQSLPKETARGVDDLTRMEMALLSGIPEEIKWSLKKYLTYSNKAPYMISLRTL
PDLLPLFKTFILPLERIVEGLNKSSICDSKAMDSLQMGLNALLILRNLAQDTDSVQILVK
DREIKSFILFILKKFQCVATGDNKWQLYEGNATFFNELTHYTLDLMEAISSYIAPAMKDD
HYFQTLVSILNYTKDRYMVISILRSLSRLLVRSKANEESAADNLDHKTLSLIVSFLLLEC
DSELIIASLDFLYQYILPGSQRITELFKSKECSLILEATLPNLLSYNIATPDYHLLQKHK
IRLIKRLKPPAPKEPPNLSEDLFQQLFKLNEPLRSTAWLRCCFEPVQEAEFTQISLWRSY
ESKFGQPVRESGRKLLPAVEFIKNVSNAFNNAAAIVITDPVTGKKRFVIKGIQPRFKALG
IADGERESQVPISALKSKFLNDSKEITPARQNSIPEVKFPQELSDVSKVACTFLCLLSND
TDDGAGSAFCQRIRPLVLHKLADIPPLTLALSEYMENTSGL
Sequence of entity 11 (I), FASTA
>6KW4_11 Chromatin structure-remodeling complex protein RSC6 (chains I)
MVTQTNPVPVTYPTDAYIPTYLPDDKVSNLADLKKLIEMDSRLDLYLTRRRLDTSINLPT
NTKTKDHPPNKEMLRIYVYNTTESSPRSDSGTPADSGKTTWTLRIEGKLLHESANGKHPF
SEFLEGVAVDFKRLKPLGMGKKRKRDSSLSLPLNLQQPEYNDQDSTMGDNDNGEDEDSAE
AESREEIVDALEWNYDENNVVEFDGIDIKRQGKDNLRCSITIQLRGVDGGKVQYSPNLAT
LIGMQTGSVNDAVYSIYKYILINNLFVTEQTEAQDGSNDAEDSSNENNNKNGAGDDDGVE
GSTPKDKPELGEVKLDSLLQKVLDTNAAHLPLMNVVQTVNKLVSPLPPIILDYTIDLSKD
TTYGATTLDVDVSHILHQPQPQPNLQKEEETDAEDTAKLREITKLALQLNSSAQKYQFFH
ELSLHPRETLTHYLWSSKQNELVLQGDQYFNEDAARTSDIYSNNNNDRSLMGNISLLYSQ
GRL
Sequence of entity 12 (G), FASTA
>6KW4_12 Chromatin structure-remodeling complex subunit SFH1 (chains G)
MSHQNQLIPQAYISNFHNRLTNEDDGIPIFTMAQQTRQHKRAKVVNYAEYDNDLFDEFNM
NGSNFNNADTHYKDNAVSHENTPALTNGVTMDGSEYNVLENMNGADSIISNNKYDAGSNM
VVESLSGLNSNNNASNGPSNKAQAQDIGNAVLPDLQDQHHNPFNILRYPKIRDTFINGKV
VSPYRLNTDQETKANANSGEAIMIPITLDIEHMGHTIKDQFLWNYNDDSISPEEFASIYC
KDLDMTSATLQTQIANIIKEQLKDLENIAATEIMSDLHVIINLTCNLQDRFFEDNFQWNL
NDKSLTPERFATSIVQDLGLTREFIPLISQSLHETILKIKKDWVDGHLIQDHVPNDAAFG
YLSGIRLDIDELGSNWCPRVEILTKEEIQKREIEKERNLRRLKRETDRLSRRGRRRLDDL
ETTMRM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structure of the RSC complex bound to the nucleosome. Ye, Y., Wu, H., Chen, K. et al. Science (2019) 366:838-843. DOI 10.1126/science.aay0033 · 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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