8AV6
Cryoem structure of ino80 core nucleosome complex in closed grappler conformation
PDB DOI: 10.2210/pdb8av6/pdb
Classification: DNA BINDING PROTEIN Organism(s): Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.)
Deposited: 2022-08-26 Deposition Author(s): Eustermann, S. , Hopfner, K.P. , Jung, J. , Kostrewa, D. , Kunert, F. , Metzner, F.J. , Schall, K. , Woike, S.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 4.68 Å
Cryoem structure of ino80 core nucleosome complex in closed grappler conformation
Eustermann, S. , Hopfner, K.P. , Jung, J. , Kostrewa, D. , Kunert, F. , Metzner, F.J. , Schall, K. , Woike, S.
Primary Citation of Related Structures: 8AV6
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| RuvB-like helicase | A | 462 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MVQISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRETKDVYEGEVTEMTPEEAENPLGGYGKTISTLLIGLKSARGQKKLRLDPSIYEAIQKERVQVGDVIYIETNTGACKRVGRSDAYATEFDLEAEEYVPIPKGEVHKKKEIVQDVTLHDLDVANARPQGGQDIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPYEPDEIRRIVRIRAQTEGVQLTDAAVDRVAEHGVRISLRYCLQLLAPASILARVNGRTQVDVQDIAEAEELFLDARRSANILTSTGESGGLHGFIS |
| RuvB-like helicase | B | 462 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MVQISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRETKDVYEGEVTEMTPEEAENPLGGYGKTISTLLIGLKSARGQKKLRLDPSIYEAIQKERVQVGDVIYIETNTGACKRVGRSDAYATEFDLEAEEYVPIPKGEVHKKKEIVQDVTLHDLDVANARPQGGQDIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPYEPDEIRRIVRIRAQTEGVQLTDAAVDRVAEHGVRISLRYCLQLLAPASILARVNGRTQVDVQDIAEAEELFLDARRSANILTSTGESGGLHGFIS |
| RuvB-like helicase | C | 462 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MVQISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRETKDVYEGEVTEMTPEEAENPLGGYGKTISTLLIGLKSARGQKKLRLDPSIYEAIQKERVQVGDVIYIETNTGACKRVGRSDAYATEFDLEAEEYVPIPKGEVHKKKEIVQDVTLHDLDVANARPQGGQDIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPYEPDEIRRIVRIRAQTEGVQLTDAAVDRVAEHGVRISLRYCLQLLAPASILARVNGRTQVDVQDIAEAEELFLDARRSANILTSTGESGGLHGFIS |
| Histone H4 | N | 102 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG |
| Histone H4 | R | 102 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG |
| Histone H2A | O | 129 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK |
| Histone H2A | S | 129 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK |
| Histone H2B type 1-C/E/F/G/I | P | 125 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK |
| Histone H2B type 1-C/E/F/G/I | T | 125 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK |
| RuvB-like helicase | D | 488 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MAAPLVTSVTETKELRGLNLIAAHSHIRGLGVDADTLEPRPSSQGLVGQEKARKAAAVVLEMIKQGKIAGRAVLIAGPPSTGKTAIAMGMAQSLGQDVPFTTLAASEIFSLEMSKTEALTQAFRKSIGVRIKEESEIMEGEVVEIQIDRSVTGGAKQGKLTIKTTDMEAIYDMGSKMIDAMTKERVMAGDIISIDKSSGKITKLGRSYARSRDYDAMGVDTKFLQCPEGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIRSEIRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSYINRALESDLAPIVIMASNRGVSRIRGTDYKSPHGLPLDFLDRVVIINTHPYTPDELRQILSIRAQEEEVDLTPDALALLTKIGQEAGLRYASNLITTSQLIAAKRRAKQVGVEDVQRSFKLFYDPARSVRFVQESEKRLIGNDGVVDFSYQGAAEAAAPTLPAAAPVDPVGGEKMDMS |
| RuvB-like helicase | E | 488 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MAAPLVTSVTETKELRGLNLIAAHSHIRGLGVDADTLEPRPSSQGLVGQEKARKAAAVVLEMIKQGKIAGRAVLIAGPPSTGKTAIAMGMAQSLGQDVPFTTLAASEIFSLEMSKTEALTQAFRKSIGVRIKEESEIMEGEVVEIQIDRSVTGGAKQGKLTIKTTDMEAIYDMGSKMIDAMTKERVMAGDIISIDKSSGKITKLGRSYARSRDYDAMGVDTKFLQCPEGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIRSEIRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSYINRALESDLAPIVIMASNRGVSRIRGTDYKSPHGLPLDFLDRVVIINTHPYTPDELRQILSIRAQEEEVDLTPDALALLTKIGQEAGLRYASNLITTSQLIAAKRRAKQVGVEDVQRSFKLFYDPARSVRFVQESEKRLIGNDGVVDFSYQGAAEAAAPTLPAAAPVDPVGGEKMDMS |
| RuvB-like helicase | F | 488 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MAAPLVTSVTETKELRGLNLIAAHSHIRGLGVDADTLEPRPSSQGLVGQEKARKAAAVVLEMIKQGKIAGRAVLIAGPPSTGKTAIAMGMAQSLGQDVPFTTLAASEIFSLEMSKTEALTQAFRKSIGVRIKEESEIMEGEVVEIQIDRSVTGGAKQGKLTIKTTDMEAIYDMGSKMIDAMTKERVMAGDIISIDKSSGKITKLGRSYARSRDYDAMGVDTKFLQCPEGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIRSEIRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSYINRALESDLAPIVIMASNRGVSRIRGTDYKSPHGLPLDFLDRVVIINTHPYTPDELRQILSIRAQEEEVDLTPDALALLTKIGQEAGLRYASNLITTSQLIAAKRRAKQVGVEDVQRSFKLFYDPARSVRFVQESEKRLIGNDGVVDFSYQGAAEAAAPTLPAAAPVDPVGGEKMDMS |
| Ino80 | G | 1856 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MDHFPTVLQRPPHFDEDGSAGTGRMRSNVVGNGSSNGARDDRGLRGGLRDILNPVGSASQTMPSASHGGTHSTPGTPGAPAPPRPHSSFSLRSPTQTGNHHASPYSAPTSSAAATSSQQPAGACSMLNNPFVTASTPFPPPPLQAPPSLASSRTSPSGLQHPPRSPLHAPPVYYPSDVRDRDLVRDQQTSLSFYDPTTDSKRDRDRERDRERERTGSDPESGAWSTSTQNSPPKIRDSYNYSRSPSFNNSGNYPSATGSYPPRSPVVRPHPAPPAGSMSPSAGSRTVTSPSLRHLAMPSTHSSQSASTVLPPLARTETPAPSARATPASNTPSRASGVMSFSNILSSSEPISKPRPTSPISLDNNPAMVARTEPAERPDKGEKDKKQSRKIIKTRVSDIKSAESTPKMTRKSAVKPETPTMLRIPTKRTANGSMKHKAFSADKEKTIRDIMDQFDYESIDETEFEDELLAWKERARRRRQEMNRRDFIHRQSRRSDFAETEALKLQIHANLGKARYSDLHYDEALQEVREQELWAEKERKKDMQRKRRREKSMAATLEQQAAALQKASQAEDEAERLKYIREAERANKKVQQTKYILQKGIKGPARNLPPIEPNLEGGTMATFSAENMEPGKVKGKGRGGRLKKSKEQKQAEKEQAELAQAAIDAGEEPPSKEETKIRIKLSKAKASAKEEAEKDKENKEPKQPKEPEKPVEEPKDPLELKFQSKGYNQIYDQIWRDLARKDVSKVFRLATDSYATKASNLKKTAILASKEAKRWQLRTNKGTKDLQARAKRVMRDMMGFWKRNEREERDLRKAAERLELENARKEEADREAARQRRKLNFLISQTELYSHFISKKIKTHEVERSTDHPDVATDEKDKIPEPTLNINVPEPTGPIAPKVTDFNSLDFDNEDESALQAAAMANAQNAIAEAQKKAREFNKDETKLDEDGEMNFQHPELTEFEVAQPKLLNCQLKEYQLKGLNWLVNLYEQGINGILADEMGLGKTVQSISVMAYLAERYDIWGPFLVVAPASTLHNWQQEVSKFVPDFKVLPYWGTAADRKVLRKFWDRKHTTYKKDSPFHVMITSYQLVVSDVAYFQKMKWQYMILDEAQAIKSSQSSRWKCLLGFHCRNRLLLTGTPIQNNMQELWALLHFIMPSLFDSHDEFSEWFSKDIESHAQSNTKLNEDQLKRLHMILKPFMLRRVKKHVQKELGDKIEIDVFCELSYRQRAMYQSLRNQISIMDLIEKATVGDNEDSATLMNLVMQFRKVCNHPDLFERADTSSPFFCGHFAETGSFLREGTNVALGYSTRSLVEYRLPRLIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPENIRSSLEGIENFTWLRFVDTSLQEAYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEITTEGVLRDLMNIARVKYRELGLCRLEKAARPRASAPPIEVVCDSRSAVIERENIMFHPAMRKALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPSMARFVTDSGKLAKLDELLRELKEGGHRVLLYFQMTRMIDLMEEYLTYRNYKYCRLDGSTKLEDRRDTVADFQTRPEIFIFLLSTRAGGLGINLTTADTVIFYDSDWNPTIDSQAMDRAHRLGQTKQVTVYRLITRGTIEERIRKRALQKEEVQRVVITGTGSVDFSGRRPPENRNRDIAMWLADDEQAEMIERREKELIESGEYDKIMQQRRKGGKRKRGAANGDTVPSLEDMYHEGEGHFDDNKGSGAATPVDADSLGRGGKRKKAGGSKKAKTTKQRLAIADGEIDDGEIDIDYKDDDDKGTDYKDDDDK |
| PAPA-1 domain-containing protein | H | 492 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MSTRPRRHAAQRASQAITDLADRDRESDHSHGPISSRMSSFNSSSRSRLPGKGIASVSRSEAGGASDPEHIHLTVKLPSSKLRQATSSSGIKKAGSVGSSSSSSGGGKAAVKRARGGKRSRVLESSEEEEEENEVEVLGDEDEEEEEEEDEIEVREGEGYDEDEEDVEDEDEEMQDLGEEDADGEDDEMDVDAEGEEDADGDVNMDAGVVGARATTVRAVPPAIKVTKPPKESPSNGKAATASKANDNAVPVKRPAPDSDDESLSSLESEPEEEVNVAGGEDAEGEDDDAEGEVDAEGEEEEEEEEIEVADEDAEGEDVEQDEDEDEEEEDDDDEMISRAQTPDMSRLTARQRARLGEASGEYLKLSDEVQSKKHFTAEELSMRRAEMARRRRNLSEKRNEEIKMETVNKLLKKQAPRTTRRAAQAAAAAEEAEEAAKQPKRPDPMMIRWVNNKMGSVVAVPEELLGTHAGVVFGAGPGKGLPAGKMVEEVS |
| YL1_C domain-containing protein | I | 219 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MSNPDAQSAQAAHQALVEQLDLHSIHKTFRNPNWRPNQRRNKTIKAILGESQRKEASSTSAVATPRADDNGGGSGADTPANNDNNDGLSTSGTSTPANGNGSGAGTPASNGQPNLAQASRSLQKLVLEKSLASAQAPDKKAANGFASSAPTATYTNIESAPSLAPMKHYCDVTGLPAPYLDPKTRLRYHNKEIFAMIRNLPQGMGEQFLEARGAHTVLK |
| DASH complex subunit DAD4 | J | 769 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIVIDNGSHSVRAGWNFEDKPRLAIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFEAGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTEAVANLPYSRKSMSEIIFECYGAPSLVYGIDSLFSFRHNQGQTGLVVSSSYSATHVIPVYNRKALLSQAIRLNWGGWHMAEYMLKLLKLKYYTGFPGKLNSSQTEHMVRDFCYVSLDYDRELAGYLDWTGLEDRERIVQYPYTEEVVVQKTEEELARIAERKKESGRRLQEQAAKMRLERLMKKEQELEYYKDIQRRMQGESKKEIKRLLDEAELKDEAALERVIRDLERSIKRARQKDLGEPEEEEVPDFSLLDVPDDQLDEAGLRQKRQQRLLKSNWEARQRAKAEKEAEKARLAEEARLDEERRKNDLEGWLEEKRQLRLAKLNQLKERERLKADLGNRKSLASQIRMKNIANLASDNPTGSGSRKRRRGGAGADQDDDFGADDADWGVYRSVAIGANKGDDSDDEEGEEDLEAAIRSLENDLLRYDKTFSYDMTLDAQRDWSKSLLHAFRYGPRPFDPSSQAETHRVHLNVERIRVPEVLFQPAAIAGVDQAGLVEIAGDILCQRLPSLPGIQDAPDAFLRDVFLTGGNTLFQNFDERLRQGLMALLPVGAPLRVRRAQDAILDAWRGAAGWACTEEAKAAWITREEYLEKGGEYIKEHDLGNAFA |
| Histone H3.2 | M | 135 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| Histone H3.2 | Q | 135 | Salmonella Enterica , Aspergillus Novofumigatus Ibt 16806 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) | ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA | k | 227 | NA | CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAGTCGGATAGTGTTCCGAGCTCCCACTCTAGAGGATCCCCGGGTACCGA |
| DNA (208-MER) | l | 227 | NA | TCGGTACCCGGGGATCCTCTAGAGTGGGAGCTCGGAACACTATCCGACTGGCACCGGCAAGGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2022-08-26 Deposition Author(s): Eustermann, S. , Hopfner, K.P. , Jung, J. , Kostrewa, D. , Kunert, F. , Metzner, F.J. , Schall, K. , Woike, S.