7EGM: The SRM module of SWI/SNF-nucleosome complex
The SRM module of SWI/SNF-nucleosome complex. Determined by electron microscopy at 3.6 Å resolution. Released 12 Jan 2022.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 8
- Atoms
- 19,819
- Mol. weight
- 704.62 kDa
- Released
- 12 Jan 2022
Explore 7EGM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7EGM contains 107 α-helices and 33 β-strands across 8 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: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 485-486 | 2 | |
| α-helix | 490-493 | 4 | |
| α-helix | 495-517 | 23 | |
| α-helix | 528-537 | 10 | |
| α-helix | 539-556 | 18 | |
| α-helix | 576-587 | 12 | |
Chain B: 24 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 679-691 | 13 | |
| β-strand | 705-706 | 2 | 1 |
| α-helix | 707-713 | 7 | |
| α-helix | 720-733 | 14 | |
| α-helix | 748-764 | 17 | |
| β-strand | 777 | 1 | 2 |
| α-helix | 794-799 | 6 | |
| α-helix | 884-895 | 12 | |
| α-helix | 910-928 | 19 | |
| α-helix | 934-937 | 4 | |
| α-helix | 943-956 | 14 | |
| α-helix | 966-982 | 17 | |
| α-helix | 991-1002 | 12 | |
| β-strand | 1006-1007 | 2 | 3 |
| β-strand | 1025-1026 | 2 | 3 |
| α-helix | 1034-1037 | 4 | |
| α-helix | 1039-1045 | 7 | |
| α-helix | 1052-1062 | 11 | |
| α-helix | 1081-1090 | 10 | |
| α-helix | 1104-1114 | 11 | |
| α-helix | 1119-1124 | 6 | |
| α-helix | 1131-1153 | 23 | |
| α-helix | 1189-1194 | 6 | |
| α-helix | 1200-1212 | 13 | |
| α-helix | 1234-1259 | 26 | |
| α-helix | 1266-1270 | 5 | |
| α-helix | 1279-1285 | 7 | |
| α-helix | 1293-1313 | 21 | |
Chain C: 13 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 370-399 | 30 | |
| α-helix | 409-410 | 2 | |
| β-strand | 426-427 | 2 | 1 |
| β-strand | 432 | 1 | 4 |
| β-strand | 435 | 1 | 4 |
| α-helix | 436-439 | 4 | |
| α-helix | 444-449 | 6 | |
| β-strand | 457-461 | 5 | 5 |
| β-strand | 476-480 | 5 | 5 |
| α-helix | 488-498 | 11 | |
| α-helix | 510-522 | 13 | |
| β-strand | 543-552 | 10 | 6 |
| β-strand | 555-564 | 10 | 6 |
| α-helix | 572-583 | 12 | |
| α-helix | 590-609 | 20 | |
| α-helix | 630-633 | 4 | |
| α-helix | 636-638 | 3 | |
| α-helix | 642-645 | 4 | |
| β-strand | 651-654 | 4 | 6 |
| α-helix | 657-662 | 6 | |
| β-strand | 729 | 1 | 6 |
| α-helix | 732-734 | 3 | |
| β-strand | 752 | 1 | 7 |
Chain D: 20 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 309-311 | 3 | |
| α-helix | 321-326 | 6 | |
| α-helix | 328-330 | 3 | |
| α-helix | 344-354 | 11 | |
| α-helix | 375-387 | 13 | |
| α-helix | 396 | 1 | |
| α-helix | 406-408 | 3 | |
| β-strand | 414-417 | 4 | 8 |
| α-helix | 424-425 | 2 | |
| α-helix | 434-436 | 3 | |
| α-helix | 438-443 | 6 | |
| α-helix | 452-467 | 16 | |
| α-helix | 519-521 | 3 | |
| α-helix | 529-541 | 13 | |
| α-helix | 546-553 | 8 | |
| α-helix | 558-566 | 9 | |
| α-helix | 590-593 | 4 | |
| α-helix | 606-614 | 9 | |
| α-helix | 620-639 | 20 | |
| α-helix | 674-740 | 67 | |
| α-helix | 763-775 | 13 | |
Chain E: 19 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 305-308 | 4 | 8 |
| α-helix | 309-311 | 3 | |
| β-strand | 320 | 1 | 2 |
| α-helix | 321-326 | 6 | |
| α-helix | 328-330 | 3 | |
| α-helix | 340-354 | 15 | |
| α-helix | 364-370 | 7 | |
| α-helix | 375-387 | 13 | |
| α-helix | 405-406 | 2 | |
| α-helix | 434-443 | 10 | |
| α-helix | 448-467 | 20 | |
| α-helix | 514-523 | 10 | |
| α-helix | 529-541 | 13 | |
| α-helix | 546-553 | 8 | |
| α-helix | 558-565 | 8 | |
| α-helix | 592-594 | 3 | |
| α-helix | 606-615 | 10 | |
| α-helix | 620-626 | 7 | |
| α-helix | 638-643 | 6 | |
| α-helix | 649-746 | 98 | |
| α-helix | 764-775 | 12 | |
Chain H: 11 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 57-59 | 3 | |
| α-helix | 71-105 | 35 | |
| β-strand | 124-132 | 9 | 9 |
| β-strand | 157-164 | 8 | 9 |
| β-strand | 184-189 | 6 | 10 |
| β-strand | 281-283 | 3 | 9 |
| β-strand | 291-298 | 8 | 10 |
| β-strand | 308-309 | 2 | 11 |
| α-helix | 314-318 | 5 | |
| β-strand | 322-323 | 2 | 11 |
| α-helix | 325-337 | 13 | |
| β-strand | 342 | 1 | 12 |
| β-strand | 378-379 | 2 | 12 |
| α-helix | 383-386 | 4 | |
| β-strand | 401-402 | 2 | 12 |
| α-helix | 403-407 | 5 | |
| β-strand | 420-427 | 8 | 10 |
| β-strand | 442-443 | 2 | 9 |
| α-helix | 458-509 | 52 | |
| α-helix | 514-520 | 7 | |
| α-helix | 523-530 | 8 | |
| α-helix | 545-548 | 4 | |
| α-helix | 550-563 | 14 | |
Chain I: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 68-80 | 13 | |
| α-helix | 103-121 | 19 | |
| α-helix | 132-135 | 4 | |
| α-helix | 141-150 | 10 | |
| α-helix | 151-153 | 3 | |
Chain J: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 231-240 | 10 | |
| α-helix | 285-293 | 9 | |
| α-helix | 304-306 | 3 | |
| β-strand | 312 | 1 | 6 |
| α-helix | 319-321 | 3 | |
| α-helix | 330-334 | 5 | |
| β-strand | 442 | 1 | 13 |
| β-strand | 447 | 1 | 13 |
| α-helix | 448-450 | 3 | |
| α-helix | 451-457 | 7 | |
| α-helix | 466-499 | 34 | |
| β-strand | 549 | 1 | 7 |
| α-helix | 562-564 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transcription regulatory protein SNF2 | A | protein | 982 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P22082 (AlphaFold model) |
| SWI/SNF chromatin-remodeling complex subunit SWI1 | B | protein | 1093 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P09547 (AlphaFold model) |
| SWI/SNF chromatin-remodeling complex subunit SNF5 | C | protein | 918 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P18480 (AlphaFold model) |
| SWI/SNF complex subunit SWI3 | D, E | protein | 836 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32591 (AlphaFold model) |
| Transcription regulatory protein SNF12 | H | protein | 566 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53628 |
| Transcription regulatory protein SNF6 | I | protein | 332 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P18888 |
| SWI/SNF global transcription activator complex subunit SWP82 | J | protein | 634 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P43554 |
Sequence of entity 1 (A), FASTA
>7EGM_1 Transcription regulatory protein SNF2 (chains A)
LQDQYKEGIKVVDIDDPDMMVDSFTMPNISHSNIDYQTLLANSDHAKFTIEPGVLPVGID
THTATDIYQTLIALNLDTTVNDCLDKLLNDECTESTRENALYDYYALQLLPLQKAVRGHV
LQFEWHQNSLLTNTHPNFLSKIRNINVQDALLTNQLYKNHELLKLERKKTEAVARLKSMN
KSAINQYNRRQDKKNKRLKFGHRLIATHTNLERDEQKRAEKKAKERLQALKANDEEAYIK
LLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMVPKMK
DEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNHLNGI
LADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTISFKG
SPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSKLSLT
LNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGGQDKI
ELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQMLKY
RRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRVAGKF
ELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSELLRLF
NAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNEVRIL
RLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERRKKRE
SGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPDIYSR
DIGAELKREESESAAVYNGRGARERKTATYNDNMSEEQWLRQFEVSDDEKNDKQARKQRT
KKEDKSEAIDGGGSGGHHHHHH
Sequence of entity 2 (B), FASTA
>7EGM_2 SWI/SNF chromatin-remodeling complex subunit SWI1 (chains B)
SNQLISNYAASNSMDRSSSASNEFVPNTSDNNNNSNNHNMRNNSNNKTSNNNNVTAVPAA
TPANTNNSTSNANTVFSERAAMFAALQQKQQQRFQALQQQQQQQQNQQQQNQQPQQQQQQ
QQNPKFLQSQRQQQQRSILQSLNPALQEKISTELNNKQYELFMKSLIENCKKRNMPLQSI
PEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESIYFRILLPYER
HMISQEGIKETQAKRIFLQQFLQELLKKVQQQQQAAALANANNNINSASSAPTPAAPGAS
VPATAAPGTEAGIVPVSANTPKSLNSNININVNNNNIGQQQVKKPRKQRVKKKTKKELEL
ERKEREDFQKRQQKLLEDQQRQQKLLLETKLRQQYEIELKKLPKVYKRSIVRNYKPLINR
LKHYNGYDINYISKIGEKIDSNKPIFLFAPELGAINLHALSMSLQSKNLGEINTALNTLL
VTSADSNLKISLVKYPELLDSLAILGMNLLSNLSQNVVPYHRNTSDYYYEDAGSNQYYVT
QHDKMVDKIFEKVNNNATLTPNDSNDEKVTILVDSLTGNQLPTPTPTEMEPDLDTECFIS
MQSTSPAVKQWDLLPEPIRFLPNQFPLKIHRTPYLTSLKKIKDEIDDPFTKINTRGAEDP
KVLINDQLSTISMILRNISFSDNNSRIMSRNFYLKRFISDLLWLVLIHPENFTCNRKILN
FKKDLVIVLSNISHLLEIASSIDCLLILILVISFGQPKLNPMASSSSFGSESLTFNEFQL
QWGKYQTFGVDILAKLFSLEKPNLNYFKSILLNKNTGNNLYDRNSNNNHKDKKLLRRLLN
LYNDNNKNNNNRHNLLNDVVSFLFSAIPLQQVLSQSADPSLLIDQFSPVISQSLTSILVI
VQKILPLSNEVFEISENNSDSNSNNNGNKDSSFNFNKNLPFVWLSSEENIGSGLLKLSEI
ILNINNSTSKNTLLQQQNYSKVLLPSINISCVQLIKCLVEKSICFENCLNNDPEILKKIA
SIPNLFPTDLEIFQLFTNPSVDIQIINQYQLLYNLKNDILTNLEGGSGGWSHPQFEKWSH
PQFEKWSHPQFEK
Sequence of entity 3 (C), FASTA
>7EGM_3 SWI/SNF chromatin-remodeling complex subunit SNF5 (chains C)
MNNQPQGTNSVPNSIGNIFSNIGTPSFNMAQIPQQLYQSLTPQQLQMIQQRHQQLLRSRL
QQQQQQQQQTSPPPQTHQSPPPPPQQSQPIANQSATSTPPPPPAPHNLHPQIGQVPLAPA
PINLPPQIAQLPLATQQQVLNKLRQQAIAKNNPQVVNAITVAQQQVQRQIEQQKGQQTAQ
TQLEQQRQLLVQQQQQQQLRNQIQRQQQQQFRHHVQIQQQQQKQQQQQQQHQQQQQQQQQ
QQQQQQQQQQQQQQQQQQQQQQQQQQQQGQIPQSQQVPQVRSMSGQPPTNVQPTIGQLPQ
LPKLNLPKYQTIQYDPPETKLPYPTYWSDKKADTDTLLYEQIIQRDKINKYSLIRETNGY
DPFSIYGFSNKEYISRLWHTLKYYQDLKNTRMKSITSTSQKIPSASIWGNGYSGYGNGIT
NTTTRVIPQVEVGNRKHYLEDKLKVYKQAMNETSEQLVPIRLEFDQDRDRFFLRDTLLWN
KNDKLIKIEDFVDDMLRDYRFEDATREQHIDTICQSIQEQIQEFQGNPYIELNQDRLGGD
DLRIRIKLDIVVGQNQLIDQFEWDISNSDNCPEEFAESMCQELELPGEFVTAIAHSIREQ
VHMYHKSLALLGYNFDGSAIEDDDIRSRMLPTITLDDVYRPAAESKIFTPNLLQISAAEL
ERLDKDKDRDTRRKRRQGRSNRRGMLALSGTSASNTSMNGVHNTVAAGNASSLPPGEILL
PDIADIPRTFRTPVPSTLMPGGVDVGPSVESYELRNTTTYKSRPDRPKPVSPPCYIIDHI
PGHSLLLSIKLPGKVNTKEEFAAAPNDTSSGTNAMLPSPESLKTKLNSNIRAGVTIPSIP
NPIANHTVTNSPNPTLQPVIPGGAASKSVPTPSLPIAPPVAPHDSEATLLTNSNNGSSNN
NTQNTGGSGGDYKDDDDK
Sequence of entity 4 (D, E), FASTA
>7EGM_4 SWI/SNF complex subunit SWI3 (chains D, E)
MENTLGEGSTVNASVDVDQHGNDNNSDSNANAAVAGVANTDTAGEESQQQDESLKDEATV
PNTRDAESEAITVTAKQQPTMQANKLDSQETPSTEESRAQNVFGQDNEDSDNLFGETESS
VSNNEANTPSIPTNPVDNENNKPAIKEDSTIQDSNGDVKNMEDVKIQKEEEPENNTVIEG
VKEESQPDENTKEMDEVEEDDEDDDQPMISPDNSIFGDTKSESKQLGNTSSVANTPSEIP
DAHKAEQEDIIEKTESVDKKVDSGEERNEQEREIMNDHSKSANPKKTTITRVEPETFEIP
QAHEIVIPSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNE
YFSVTTARRNVSGDAAALFRLHKFLTKWGLINYQVDSKLLPKNIEPPLTSQYSTRHDAPR
GLFPFESYKPSVQLPDMAKLKKMMNTSDSESTLYKYLKESKRKYDEITHPPSTTDDENGD
KNDNGGKMNNEVSTSTSMTGDANLLEEGETSRPLKKVKILEQIDENWSKEDLQKLLKGIQ
EFGADWYKVAKNVGNKSPEQCILRFLQLPIEDKFLYGDGNGKGDNDNGLGPLKYAPHLPF
SKSENPVLSTIAFLVGLVNPKTVQSMTQRAIQSAESIKSQKEEISDQKPIEHIKEGSEIA
ISSLGYRSHIFATNEERQMNFLTNELIRLQMEKLDAKLNHLKKLEKFMELERKTLERQQE
NLLIQRLNFNQNSSKIVNVLSKCLNLISDSNINNSSVAEKEEIRSQIDHFKSMLSKPETL
SIGKNPFNKPNIETGENHNGQSISNENDVKPISIEAPQFYRYWSAGGSGGHHHHHH
Sequence of entity 5 (H), FASTA
>7EGM_5 Transcription regulatory protein SNF12 (chains H)
MSKVMKPSNGKGSRKSSKAATPDTKNFFHAKKKDPVNQDKANNASQITPTVPHSHPSDMV
IPDHLAELIPELYSFQQLVDSEKRLDHFIHLRNLHMKRMVAQWERSKLSQEFLYPHLNFP
NVKFLRIFISNVSENQPWQMDTNNEADLMALENATWTMRIEGRLLDNVQANDPAREKFSS
FIESIVVDFKNKENDNVPSTKFNAAPEENATEGPSDKKLNLNLPLQFSLPNGDNSTTTNT
DQNNATMGEETAKKDMSSTTPKLESVKWQYDPNNPVDFDGLDIKRVGSENVECTISILRK
SSPEEPFMSYSPQLTAIIGLKSGTSHDAIFSIYKYIHLNELLTNDESAFENLMGNRNNHN
SNTSTSKMLDAASSQVSIVKLDTQLITLLPSSLKESSPDTMKLTDLLSLINSTHLLPLQP
IEIDYTVRVDKASTYGELVLDIEVPDVNALKFNNTQRESQIGAAELNENARELEQIKPKI
ALQDKEITSVLSNLHESNKRYRFFKKISEDPVKALNECIASTSNALKVLSGDEGYNEDMV
RRANFYKENEAMLRENIEVILSNGRM
Sequence of entity 6 (I), FASTA
>7EGM_6 Transcription regulatory protein SNF6 (chains I)
MGVIKKKRSHHGKASRQQYYSGVQVGGVGSMGAINNNIPSLTSFAEENNYQYGYSGSSAG
MNGRSLTYAQQQLNKQRQDFERVRLRPEQLSNIIHDESDTISFRSNLLKNFISSNDAFNM
LSLTTVPCDRIEKSRLFSEKTIRYLMQKQHEMKTQAAELQEKPLTPLKYTKLIAAAEDGS
RSTKDMIDAVFEQDSHLRYQPDGVVVHRDDPALVGKLRGDLREAPADYWTHAYRDVLAQY
HEAKERIRQKEVTAGEAQDEASLQQQQQQDLQQQQQVVTTVASQSPHATATEKEPVPAVV
DDPLENMFGDYSNEPFNTNFDDEFGDLDAVFF
Sequence of entity 7 (J), FASTA
>7EGM_7 SWI/SNF global transcription activator complex subunit SWP82 (chains J)
MLGEDEGNTVLEKGNNPSVKQGEVGAVFIVPKILIREHERVILKQILQILDQDELVQPPL
DKFPYKKLELPKYIDELKTRDATNTSYKMIQLDAYGEKKVGSNGELFGGRHYLFNTFTFT
AHMGVLLVLLQDVIKVLYQSNATHDEDEFIVQHDQILVMETSEEQTKFLAKNGVIPEESK
GSFKYITARSAFVEFGASVIAGGQRIVDDYWESLAKKQNLSSHQRVFKLSTNLISKISLL
RPSFQNNRISNANEISANTNNTCTISTSKFESQYPIVTEQPSAEIREAYIENFAKGEHIS
AIVPGQSISGTLELSAQFRVPRYHSKNSFQQALQMKAMDIPIGRHEELLAQYESQAPDGS
ASISLPNHIPSVNPSNKPIKRMLSSILDINVSSSKNKKSEENEMIKPMNKGQHKNNTSLN
INGWKFESLPLKSAENSGKQQYYRGLPLYEKNTLLERLKQLTPNEIKELEHLHDAVFVNT
GLQNVRKVRTKKWKKYWQYKAGIPIGLKRSQLDEFKNKYLKDVLAQTSVTTNFNEITNTD
ETITTKRVPNPNFLGNCNIKDFKPPYIYSHVNKVPQNVAGDKTAVKLDTEVKNTNANPVV
ATDPVAAKPDNLANFSNEVAMNNGGSGGHHHHHH
Primary citation
Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity. He, Z.Y., Chen, K.J., Ye, Y.P. et al. Cell Discov (2021) 7:28-28. DOI 10.1038/s41421-021-00262-5 · PubMed
Other PDB entries of the same protein (UniProt P22082 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7VRC 2.15 Å, Structure of the Yeast SNF11/SNF2 complex
- 4I6M 2.8 Å, Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.
- 7C4J 2.89 Å, Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state
- 6IY2 3.47 Å, Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state
- 5Z3O 3.62 Å, Structure of Snf2-nucleosome complex in ADP state
- 6IY3 3.67 Å, Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
- 5X0X 3.97 Å, Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome
- 9PB3 4.0 Å, ARP of SWI/SNF of PIC-Med-SWI/SNF
- 5Z3V 4.22 Å, Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state
- 5Z3L 4.31 Å, Structure of Snf2-nucleosome complex in apo state
- 5Z3U 4.31 Å, Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state
- 5X0Y 4.69 Å, Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome
Browse structure collections
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