8OOC: RuvB-like helicase

CryoEM Structure INO80core Hexasome complex Rvb core refinement state1. Determined by electron microscopy at 2.93 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 2.93 Å
Organism: Thermochaetoides thermophila
Chains: 10
Atoms: 28,371
Mol. weight: 609.22 kDa
Ligands: ATP, MG, ADP
Released: 2 Aug 2023

Explore 8OOC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OOC contains 205 α-helices and 204 β-strands across 10 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: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
β-strand	27	1	2
α-helix	32	1
β-strand	33	1	2
α-helix	34	1
β-strand	36-37	2	3
β-strand	40-41	2	3
α-helix	44-58	15
β-strand	62	1	4
β-strand	66-70	5	5
α-helix	77-87	11
β-strand	94-98	5	5
α-helix	99-101	3
α-helix	109-119	11
β-strand	121-144	24	6
β-strand	154-164	11	6
β-strand	167-173	7	6
α-helix	175-183	9
β-strand	190-195	6	6
β-strand	200-207	8	6
β-strand	215	1	7
β-strand	221-222	2	6
α-helix	223-226	4
β-strand	230-240	11	6
α-helix	241-249	9
α-helix	257-264	8
α-helix	266-267	2
α-helix	274-289	16
β-strand	293-297	5	6
β-strand	299-303	5	5
α-helix	305-307	3
α-helix	310-320	11
β-strand	327-332	6	5
β-strand	334	1	8
β-strand	336-339	4	9
β-strand	342-348	7	9
α-helix	353-356	4
β-strand	359-363	5	5
α-helix	366-368	3
α-helix	369-382	14
β-strand	387	1	10
α-helix	389-395	7
α-helix	404-420	17
β-strand	426	1	10
α-helix	428-437	10
β-strand	439	1	11
α-helix	441-451	11
α-helix	460	1
β-strand	461	1	12

Chain B: 24 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	13
β-strand	27	1	14
α-helix	32	1
β-strand	33	1	14
α-helix	34	1
β-strand	36-37	2	15
β-strand	40-41	2	15
α-helix	44-59	16
β-strand	62	1	16
β-strand	66-70	5	17
α-helix	77-87	11
β-strand	94-98	5	17
α-helix	109-119	11
β-strand	121-141	21	18
β-strand	158-164	7	18
β-strand	167-173	7	18
α-helix	175-183	9
β-strand	190-195	6	18
β-strand	201-207	7	18
α-helix	208-210	3
β-strand	216	1	19
β-strand	221-222	2	18
α-helix	223-225	3
β-strand	230-240	11	18
α-helix	241-249	9
α-helix	253-255	3
α-helix	258-261	4
α-helix	263-265	3
α-helix	274-289	16
β-strand	293-297	5	18
β-strand	299-303	5	17
α-helix	305-307	3
β-strand	309	1	20
α-helix	310-319	10
α-helix	325-326	2
β-strand	327-332	6	17
β-strand	334	1	21
β-strand	336-339	4	22
β-strand	340	1	20
β-strand	342-348	7	22
α-helix	353-356	4
β-strand	359-363	5	17
α-helix	366-368	3
α-helix	369-382	14
β-strand	387	1	23
α-helix	389-401	13
α-helix	404-420	17
β-strand	426	1	23
α-helix	428-437	10
β-strand	439	1	24
α-helix	441-451	11
α-helix	459-460	2
β-strand	461	1	25

Chain C: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	26
β-strand	16	1	27
β-strand	27	1	28
α-helix	32	1
β-strand	33	1	28
α-helix	34	1
β-strand	36-37	2	29
β-strand	40-41	2	29
α-helix	44-58	15
β-strand	66-71	6	30
α-helix	77-88	12
β-strand	94-98	5	30
α-helix	99-102	4
α-helix	109-119	11
β-strand	121-143	23	7
α-helix	144	1
α-helix	147-148	2
β-strand	153-164	12	7
β-strand	167-173	7	7
α-helix	175-177	3
α-helix	178-184	7
β-strand	190-195	6	7
β-strand	201-207	7	7
α-helix	208-210	3
β-strand	216	1	26
β-strand	221-222	2	7
α-helix	223-225	3
β-strand	230-240	11	7
α-helix	241-249	9
α-helix	257-262	6
α-helix	274-290	17
β-strand	293-297	5	7
β-strand	299-303	5	30
α-helix	305-307	3
α-helix	310-320	11
β-strand	327-332	6	30
β-strand	336-339	4	31
β-strand	342-348	7	31
α-helix	353-356	4
β-strand	359-364	6	30
α-helix	369-383	15
β-strand	387	1	32
α-helix	389-401	13
α-helix	404-420	17
β-strand	426	1	32
α-helix	428-437	10
β-strand	439	1	33
α-helix	441-451	11
α-helix	459-460	2
β-strand	461	1	34

Chain D: 22 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	35
α-helix	38	1
β-strand	39	1	35
α-helix	40	1
β-strand	42-43	2	36
β-strand	46-47	2	36
α-helix	50-65	16
β-strand	68	1	1
β-strand	72-76	5	11
α-helix	83-94	12
β-strand	100-104	5	11
α-helix	105-108	4
α-helix	115-124	10
β-strand	127-150	24	7
β-strand	156-163	8	7
β-strand	168-173	6	7
α-helix	175-183	9
β-strand	190-195	6	7
β-strand	201-206	6	7
α-helix	209-210	2
β-strand	223	1	7
α-helix	225-227	3
β-strand	232-242	11	7
α-helix	243-250	8
α-helix	258-261	4
α-helix	269-284	16
β-strand	288-292	5	7
β-strand	294-298	5	11
α-helix	300-302	3
β-strand	304	1	37
α-helix	305-314	10
β-strand	322-327	6	11
β-strand	329	1	12
β-strand	331-333	3	38
α-helix	334	1
β-strand	335	1	37
β-strand	340-342	3	38
α-helix	347-350	4
β-strand	353-357	5	11
α-helix	360-362	3
α-helix	363-376	14
β-strand	381	1	39
α-helix	383-395	13
α-helix	398-414	17
β-strand	420	1	39
α-helix	422-431	10
β-strand	433	1	30
α-helix	435-443	9

Chain E: 26 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	4
β-strand	32-33	2	40
β-strand	38-39	2	40
α-helix	40	1
β-strand	42-43	2	41
β-strand	46-47	2	41
α-helix	50-65	16
β-strand	68	1	13
β-strand	72-76	5	24
α-helix	83-94	12
α-helix	95-97	3
β-strand	100-104	5	24
α-helix	105-108	4
α-helix	115-124	10
β-strand	127-147	21	42
β-strand	158-163	6	42
β-strand	168-172	5	42
β-strand	173	1	19
α-helix	174	1
α-helix	175-183	9
β-strand	190-195	6	42
β-strand	201-206	6	42
β-strand	207	1	43
α-helix	208-213	6
β-strand	224	1	43
β-strand	232-242	11	42
α-helix	243-249	7
α-helix	255-257	3
α-helix	258-261	4
α-helix	269-284	16
β-strand	288-292	5	42
β-strand	294-298	5	24
α-helix	300-302	3
β-strand	304	1	44
α-helix	305-314	10
β-strand	322-327	6	24
β-strand	329	1	25
β-strand	331-333	3	45
α-helix	334	1
β-strand	335	1	44
β-strand	340-342	3	45
α-helix	347-350	4
β-strand	353-357	5	24
α-helix	358-362	5
α-helix	363-376	14
α-helix	380	1
β-strand	381	1	46
α-helix	382	1
α-helix	383-396	14
α-helix	398-414	17
β-strand	420	1	46
α-helix	422-431	10
β-strand	433	1	5
α-helix	435-444	10
β-strand	450	1	8
α-helix	451	1

Chain F: 24 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	16
β-strand	32	1	47
β-strand	39	1	47
β-strand	42-43	2	48
β-strand	46-47	2	48
α-helix	50-65	16
β-strand	68	1	27
β-strand	72-76	5	33
α-helix	83-94	12
β-strand	100-104	5	33
α-helix	105-108	4
α-helix	115-125	11
β-strand	127-148	22	26
β-strand	157-163	7	26
β-strand	168-173	6	26
α-helix	175-183	9
α-helix	186-187	2
β-strand	190-195	6	26
β-strand	201-207	7	26
α-helix	208-212	5
β-strand	216	1	18
β-strand	223-224	2	26
α-helix	225-227	3
β-strand	232-242	11	26
α-helix	243-251	9
α-helix	255-257	3
α-helix	258-261	4
α-helix	269-285	17
β-strand	289-292	4	26
β-strand	294-298	5	33
α-helix	300-302	3
β-strand	304	1	49
α-helix	305-314	10
α-helix	320-321	2
β-strand	322-327	6	33
β-strand	329	1	34
β-strand	331-333	3	50
α-helix	334	1
β-strand	335	1	49
β-strand	340-342	3	50
α-helix	347-350	4
β-strand	354-357	4	33
α-helix	358-360	3
α-helix	363-376	14
β-strand	381	1	51
α-helix	383-396	14
α-helix	398-414	17
β-strand	420	1	51
α-helix	422-431	10
β-strand	433	1	17
α-helix	435-444	10
α-helix	446-448	3
β-strand	450	1	21

Chain G: 27 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1224-1234	11
α-helix	1236-1239	4
α-helix	1257-1269	13
α-helix	1271-1274	4
β-strand	1280	1	52
β-strand	1283-1284	2	53
β-strand	1286-1287	2	54
α-helix	1289-1291	3
β-strand	1300-1303	4	6
β-strand	1308-1309	2	54
β-strand	1312-1314	3	55
α-helix	1317-1320	4
α-helix	1334-1341	8
α-helix	1342-1346	5
α-helix	1352-1356	5
β-strand	1361	1	26
α-helix	1366-1369	4
α-helix	1375-1383	9
α-helix	1386-1393	8
α-helix	1399-1406	8
α-helix	1418-1420	3
α-helix	1424-1427	4
α-helix	1430-1434	5
α-helix	1441-1445	5
α-helix	1448-1455	8
α-helix	1462-1463	2
β-strand	1469-1470	2	53
α-helix	1472-1474	3
β-strand	1475-1477	3	55
α-helix	1481-1491	11
α-helix	1494-1501	8
α-helix	1505-1513	9
α-helix	1528-1530	3
β-strand	1541	1	52
α-helix	1545-1550	6
α-helix	1553-1567	15
α-helix	1580-1592	13

Chain H: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	442-444	3
β-strand	447-453	7	7
β-strand	456-461	6	7
α-helix	469-474	6

2 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
RuvB-like helicase	A, B, C	protein	462	Thermochaetoides thermophila	G0RYI5 (AlphaFold model)
RuvB-like helicase	D, E, F	protein	488	Thermochaetoides thermophila	G0RYC2 (AlphaFold model)
Chromatin-remodeling ATPase Ino80	G	protein	1134	Thermochaetoides thermophila
INO80 complex subunit B-like conserved region domain-containing protein	H	protein	492	Thermochaetoides thermophila	G0RY01 (AlphaFold model)
Vps72/YL1 C-terminal domain-containing protein	I	protein	219	Thermochaetoides thermophila	G0S590 (AlphaFold model)
DASH complex subunit DAD4	J	protein	769	Thermochaetoides thermophila	G0S589

Sequence of entity 1 (A, B, C), FASTA

>8OOC_1 RuvB-like helicase (chains A, B, C)
MVQISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAH
KMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRA
IGLRVRETKDVYEGEVTEMTPEEAENPLGGYGKTISTLLIGLKSARGQKKLRLDPSIYEA
IQKERVQVGDVIYIETNTGACKRVGRSDAYATEFDLEAEEYVPIPKGEVHKKKEIVQDVT
LHDLDVANARPQGGQDIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVL
FIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLL
IIPTHPYEPDEIRRIVRIRAQTEGVQLTDAAVDRVAEHGVRISLRYCLQLLAPASILARV
NGRTQVDVQDIAEAEELFLDARRSANILTSTGESGGLHGFIS

Sequence of entity 2 (D, E, F), FASTA

>8OOC_2 RuvB-like helicase (chains D, E, F)
MAAPLVTSVTETKELRGLNLIAAHSHIRGLGVDADTLEPRPSSQGLVGQEKARKAAAVVL
EMIKQGKIAGRAVLIAGPPSTGKTAIAMGMAQSLGQDVPFTTLAASEIFSLEMSKTEALT
QAFRKSIGVRIKEESEIMEGEVVEIQIDRSVTGGAKQGKLTIKTTDMEAIYDMGSKMIDA
MTKERVMAGDIISIDKSSGKITKLGRSYARSRDYDAMGVDTKFLQCPEGELQKRKEVVHT
VSLHEIDVINSRTQGFLALFSGDTGEIRSEIRDQINTKVAEWKEEGKAEIVPGVLFIDEV
HMLDIECFSYINRALESDLAPIVIMASNRGVSRIRGTDYKSPHGLPLDFLDRVVIINTHP
YTPDELRQILSIRAQEEEVDLTPDALALLTKIGQEAGLRYASNLITTSQLIAAKRRAKQV
GVEDVQRSFKLFYDPARSVRFVQESEKRLIGNDGVVDFSYQGAAEAAAPTLPAAAPVDPV
GGEKMDMS

Sequence of entity 3 (G), FASTA

>8OOC_3 Chromatin-remodeling ATPase Ino80 (chains G)
LELKFQSKGYNQIYDQIWRDLARKDVSKVFRLATDSYATKASNLKKTAILASKEAKRWQL
RTNKGTKDLQARAKRVMRDMMGFWKRNEREERDLRKAAERLELENARKEEADREAARQRR
KLNFLISQTELYSHFISKKIKTHEVERSTDHPDVATDEKDKIPEPTLNINVPEPTGPIAP
KVTDFNSLDFDNEDESALQAAAMANAQNAIAEAQKKAREFNKDETKLDEDGEMNFQHPEL
TEFEVAQPKLLNCQLKEYQLKGLNWLVNLYEQGINGILADEMGLGKTVQSISVMAYLAER
YDIWGPFLVVAPASTLHNWQQEVSKFVPDFKVLPYWGTAADRKVLRKFWDRKHTTYKKDS
PFHVMITSYQLVVSDVAYFQKMKWQYMILDEAQAIKSSQSSRWKCLLGFHCRNRLLLTGT
PIQNNMQELWALLHFIMPSLFDSHDEFSEWFSKDIESHAQSNTKLNEDQLKRLHMILKPF
MLRRVKKHVQKELGDKIEIDVFCELSYRQRAMYQSLRNQISIMDLIEKATVGDNEDSATL
MNLVMQFRKVCNHPDLFERADTSSPFFCGHFAETGSFLREGTNVALGYSTRSLVEYRLPR
LIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPENIRSSLEGIENFTWLRFVDTSLQE
AYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEIT
TEGVLRDLMNIARVKYRELGLCRLEKAARPRASAPPIEVVCDSRSAVIERENIMFHPAMR
KALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPSMARFVTDSGKLAK
LDELLRELKEGGHRVLLYFQMTRMIDLMEEYLTYRNYKYCRLDGSTKLEDRRDTVADFQT
RPEIFIFLLSTRAGGLGINLTTADTVIFYDSDWNPTIDSQAMDRAHRLGQTKQVTVYRLI
TRGTIEERIRKRALQKEEVQRVVITGTGSVDFSGRRPPENRNRDIAMWLADDEQAEMIER
REKELIESGEYDKIMQQRRKGGKRKRGAANGDTVPSLEDMYHEGEGHFDDNKGSGAATPV
DADSLGRGGKRKKAGGSKKAKTTKQRLAIADGEIDIDYKDDDDKGTDYKDDDDK

Sequence of entity 4 (H), FASTA

>8OOC_4 INO80 complex subunit B-like conserved region domain-containing protein (chains H)
MSTRPRRHAAQRASQAITDLADRDRESDHSHGPISSRMSSFNSSSRSRLPGKGIASVSRS
EAGGASDPEHIHLTVKLPSSKLRQATSSSGIKKAGSVGSSSSSSGGGKAAVKRARGGKRS
RVLESSEEEEEENEVEVLGDEDEEEEEEEDEIEVREGEGYDEDEEDVEDEDEEMQDLGEE
DADGEDDEMDVDAEGEEDADGDVNMDAGVVGARATTVRAVPPAIKVTKPPKESPSNGKAA
TASKANDNAVPVKRPAPDSDDESLSSLESEPEEEVNVAGGEDAEGEDDDAEGEVDAEGEE
EEEEEEIEVADEDAEGEDVEQDEDEDEEEEDDDDEMISRAQTPDMSRLTARQRARLGEAS
GEYLKLSDEVQSKKHFTAEELSMRRAEMARRRRNLSEKRNEEIKMETVNKLLKKQAPRTT
RRAAQAAAAAEEAEEAAKQPKRPDPMMIRWVNNKMGSVVAVPEELLGTHAGVVFGAGPGK
GLPAGKMVEEVS

Sequence of entity 5 (I), FASTA

>8OOC_5 Vps72/YL1 C-terminal domain-containing protein (chains I)
MSNPDAQSAQAAHQALVEQLDLHSIHKTFRNPNWRPNQRRNKTIKAILGESQRKEASSTS
AVATPRADDNGGGSGADTPANNDNNDGLSTSGTSTPANGNGSGAGTPASNGQPNLAQASR
SLQKLVLEKSLASAQAPDKKAANGFASSAPTATYTNIESAPSLAPMKHYCDVTGLPAPYL
DPKTRLRYHNKEIFAMIRNLPQGMGEQFLEARGAHTVLK

Sequence of entity 6 (J), FASTA

>8OOC_6 DASH complex subunit DAD4 (chains J)
MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIV
IDNGSHSVRAGWNFEDKPRLAIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFE
AGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTEAVANLPYSRKSMSEIIFECY
GAPSLVYGIDSLFSFRHNQGQTGLVVSSSYSATHVIPVYNRKALLSQAIRLNWGGWHMAE
YMLKLLKLKYYTGFPGKLNSSQTEHMVRDFCYVSLDYDRELAGYLDWTGLEDRERIVQYP
YTEEVVVQKTEEELARIAERKKESGRRLQEQAAKMRLERLMKKEQELEYYKDIQRRMQGE
SKKEIKRLLDEAELKDEAALERVIRDLERSIKRARQKDLGEPEEEEVPDFSLLDVPDDQL
DEAGLRQKRQQRLLKSNWEARQRAKAEKEAEKARLAEEARLDEERRKNDLEGWLEEKRQL
RLAKLNQLKERERLKADLGNRKSLASQIRMKNIANLASDNPTGSGSRKRRRGGAGADQDD
DFGADDADWGVYRSVAIGANKGDDSDDEEGEEDLEAAIRSLENDLLRYDKTFSYDMTLDA
QRDWSKSLLHAFRYGPRPFDPSSQAETHRVHLNVERIRVPEVLFQPAAIAGVDQAGLVEI
AGDILCQRLPSLPGIQDAPDAFLRDVFLTGGNTLFQNFDERLRQGLMALLPVGAPLRVRR
AQDAILDAWRGAAGWACTEEAKAAWITREEYLEKGGEYIKEHDLGNAFA

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6

Primary citation

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Zhang, M., Jungblut, A., Kunert, F. et al. Science (2023) 381:313-319. DOI 10.1126/science.adf6287 · PubMed

Other PDB entries of the same protein (UniProt G0RYI5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OOP 2.7 Å, CryoEM Structure INO80core Hexasome complex composite model state2
8OO7 2.8 Å, CryoEM Structure INO80core Hexasome complex composite model state1
8OOR 2.87 Å, CryoEM Structure INO80core Hexasome complex Rvb core refinement state2
5FM7 2.9 Å, Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(ADP)
4WW4 2.94 Å, Double-heterohexameric rings of full-length Rvb1(ADP)/Rvb2(ADP)
5FM6 3.0 Å, Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(apo)
4WVY 3.64 Å, Double-heterohexameric rings of full-length Rvb1(ATP)/Rvb2(apo)
6FHS 3.75 Å, CryoEM Structure of INO80core
6FML 4.34 Å, CryoEM Structure INO80core Nucleosome complex
8AV6 4.68 Å, CryoEM structure of INO80 core nucleosome complex in closed grappler conformation

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