8OOR: RuvB-like protein 1

CryoEM Structure INO80core Hexasome complex Rvb core refinement state2. Determined by electron microscopy at 2.87 Å resolution. Released 26 Jul 2023.

Method: Electron microscopy
Resolution: 2.87 Å
Organism: Thermochaetoides thermophila
Chains: 10
Atoms: 28,371
Mol. weight: 609.22 kDa
Ligands: ADP, ATP, MG
Released: 26 Jul 2023

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

Secondary structure: helices and β-sheets

8OOR contains 217 α-helices and 209 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: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
β-strand	27	1	2
β-strand	33	1	2
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	77-88	12
β-strand	94-98	5	5
α-helix	99-102	4
α-helix	109-119	11
β-strand	121-144	24	6
β-strand	154-163	10	6
β-strand	168-173	6	6
α-helix	175-183	9
β-strand	190-195	6	6
β-strand	200-207	8	6
α-helix	208-210	3
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	257-262	6
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	310-319	10
β-strand	327-332	6	5
β-strand	334	1	8
β-strand	336-338	3	9
α-helix	339	1
β-strand	346-348	3	9
α-helix	353-356	4
β-strand	359-363	5	5
α-helix	366-368	3
α-helix	369-383	15
β-strand	387	1	10
α-helix	389-401	13
α-helix	404-409	6
α-helix	411-420	10
β-strand	426	1	10
α-helix	428-437	10
β-strand	439	1	11
α-helix	441-451	11
α-helix	456-458	3
α-helix	460	1
β-strand	461	1	12

Chain B: 26 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	44-58	15
β-strand	62	1	16
β-strand	66-71	6	17
α-helix	77-87	11
β-strand	94-98	5	17
α-helix	99-102	4
α-helix	109-119	11
β-strand	121-141	21	18
α-helix	157	1
β-strand	158-164	7	18
β-strand	167-173	7	18
α-helix	174	1
α-helix	175-183	9
β-strand	190-195	6	18
β-strand	200-207	8	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
β-strand	327-332	6	17
β-strand	334	1	21
β-strand	337-339	3	22
β-strand	340	1	20
β-strand	342-347	6	22
α-helix	348-350	3
α-helix	353-356	4
β-strand	359-364	6	17
α-helix	365-368	4
α-helix	369-383	15
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
β-strand	461	1	25

Chain C: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	26
α-helix	13-15	3
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	44-59	16
β-strand	62	1	30
β-strand	66-71	6	31
α-helix	77-88	12
β-strand	94-98	5	31
α-helix	99-102	4
α-helix	109-119	11
β-strand	121-143	23	7
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	257-264	8
α-helix	274-290	17
β-strand	293-297	5	7
β-strand	299-303	5	31
α-helix	305-307	3
α-helix	310-321	12
β-strand	327-332	6	31
β-strand	336-339	4	32
β-strand	342-348	7	32
α-helix	353-356	4
β-strand	359-364	6	31
α-helix	365-368	4
α-helix	369-383	15
β-strand	386-387	2	33
α-helix	389-401	13
α-helix	404-409	6
α-helix	411-419	9
β-strand	425-426	2	33
α-helix	428-437	10
β-strand	439	1	34
α-helix	441-450	10
α-helix	451-453	3
α-helix	460	1
β-strand	461	1	35

Chain D: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	30
β-strand	32	1	36
α-helix	38	1
β-strand	39	1	36
α-helix	40	1
β-strand	42-43	2	37
β-strand	46-47	2	37
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	115-125	11
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	209-211	3
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	38
α-helix	305-314	10
α-helix	320-321	2
β-strand	322-327	6	11
β-strand	329	1	12
β-strand	331-333	3	39
α-helix	334	1
β-strand	335	1	38
β-strand	340-342	3	39
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	40
α-helix	383-396	14
α-helix	398-414	17
β-strand	420	1	40
α-helix	422-431	10
β-strand	433	1	31
α-helix	435-443	9
α-helix	450-451	2

Chain E: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	4
β-strand	32	1	41
α-helix	38	1
β-strand	39	1	41
α-helix	40	1
β-strand	42-43	2	42
β-strand	46-47	2	42
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	127-148	22	43
β-strand	157-163	7	43
β-strand	168-172	5	43
β-strand	173	1	19
α-helix	175-183	9
β-strand	190-195	6	43
β-strand	200-206	7	43
β-strand	207	1	44
α-helix	208-210	3
β-strand	224	1	44
α-helix	225-226	2
β-strand	232-242	11	43
α-helix	243-249	7
α-helix	255-257	3
α-helix	258-261	4
α-helix	269-285	17
β-strand	289-292	4	43
β-strand	294-298	5	24
α-helix	300-302	3
β-strand	304	1	45
α-helix	305-314	10
β-strand	322-327	6	24
β-strand	329	1	25
β-strand	331-333	3	46
α-helix	334	1
β-strand	335	1	45
β-strand	340-342	3	46
α-helix	347-350	4
β-strand	353-357	5	24
α-helix	359-362	4
α-helix	363-376	14
β-strand	381	1	47
α-helix	383-396	14
α-helix	398-414	17
β-strand	420	1	47
α-helix	422-431	10
β-strand	433	1	5
α-helix	435-444	10
β-strand	450	1	8

Chain F: 23 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	16
β-strand	32-33	2	48
β-strand	38-39	2	48
α-helix	40	1
β-strand	42-43	2	49
β-strand	46-47	2	49
α-helix	50-65	16
β-strand	68	1	27
β-strand	72-76	5	34
α-helix	83-94	12
β-strand	100-104	5	34
α-helix	105-108	4
α-helix	115-124	10
β-strand	127-147	21	26
β-strand	158-163	6	26
β-strand	168-173	6	26
α-helix	174	1
α-helix	175-183	9
β-strand	190-195	6	26
β-strand	200-207	8	26
α-helix	208-213	6
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	269-284	16
β-strand	289-292	4	26
β-strand	294-298	5	34
α-helix	300-302	3
β-strand	304	1	50
α-helix	305-314	10
β-strand	322-327	6	34
β-strand	329	1	35
β-strand	331-333	3	51
α-helix	334	1
β-strand	335	1	50
β-strand	340-342	3	51
α-helix	347-350	4
β-strand	353-357	5	34
α-helix	360-362	3
α-helix	363-376	14
β-strand	381	1	52
α-helix	383-396	14
α-helix	398-414	17
β-strand	420	1	52
α-helix	422-431	10
β-strand	433	1	17
α-helix	435-444	10
β-strand	450	1	21

Chain G: 29 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1224-1240	17
α-helix	1257-1269	13
α-helix	1271-1274	4
β-strand	1280	1	53
α-helix	1282	1
β-strand	1283-1284	2	54
β-strand	1286-1287	2	55
β-strand	1300-1303	4	6
β-strand	1308-1309	2	55
β-strand	1312-1314	3	56
α-helix	1317-1320	4
β-strand	1330	1	57
β-strand	1333	1	57
α-helix	1334-1341	8
α-helix	1342-1346	5
α-helix	1352-1355	4
α-helix	1356-1358	3
β-strand	1361	1	26
α-helix	1366-1370	5
α-helix	1375-1383	9
α-helix	1386-1392	7
α-helix	1393-1395	3
α-helix	1399-1406	8
α-helix	1410-1412	3
α-helix	1418-1420	3
α-helix	1424-1427	4
α-helix	1430-1434	5
β-strand	1437	1	7
α-helix	1441-1445	5
α-helix	1448-1455	8
α-helix	1462-1463	2
β-strand	1469-1470	2	54
α-helix	1472-1474	3
β-strand	1475-1477	3	56
α-helix	1481-1491	11
α-helix	1494-1501	8
α-helix	1505-1513	9
α-helix	1528-1530	3
β-strand	1541	1	53
α-helix	1545-1550	6
α-helix	1553-1565	13
α-helix	1579-1592	14

Chain H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
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 protein 1	A, B, C	protein	462	Thermochaetoides thermophila	G0RYI5 (AlphaFold model)
RuvB-like protein 2	D, E, F	protein	488	Thermochaetoides thermophila	G0RYC2 (AlphaFold model)
Chromatin-remodeling ATPase Ino80	G	protein	1134	Thermochaetoides thermophila
Ino eighty subunit 2	H	protein	492	Thermochaetoides thermophila	G0RY01 (AlphaFold model)
Chromatin-remodeling complex subunit IES6	I	protein	219	Thermochaetoides thermophila	G0S590 (AlphaFold model)
Actin-related protein 5	J	protein	769	Thermochaetoides thermophila	G0S589

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

>8OOR_1 RuvB-like protein 1 (chains A, B, C)
MVQISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAH
KMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRA
IGLRVRETKDVYEGEVTEMTPEEAENPLGGYGKTISTLLIGLKSARGQKKLRLDPSIYEA
IQKERVQVGDVIYIETNTGACKRVGRSDAYATEFDLEAEEYVPIPKGEVHKKKEIVQDVT
LHDLDVANARPQGGQDIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVL
FIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLL
IIPTHPYEPDEIRRIVRIRAQTEGVQLTDAAVDRVAEHGVRISLRYCLQLLAPASILARV
NGRTQVDVQDIAEAEELFLDARRSANILTSTGESGGLHGFIS

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

>8OOR_2 RuvB-like protein 2 (chains D, E, F)
MAAPLVTSVTETKELRGLNLIAAHSHIRGLGVDADTLEPRPSSQGLVGQEKARKAAAVVL
EMIKQGKIAGRAVLIAGPPSTGKTAIAMGMAQSLGQDVPFTTLAASEIFSLEMSKTEALT
QAFRKSIGVRIKEESEIMEGEVVEIQIDRSVTGGAKQGKLTIKTTDMEAIYDMGSKMIDA
MTKERVMAGDIISIDKSSGKITKLGRSYARSRDYDAMGVDTKFLQCPEGELQKRKEVVHT
VSLHEIDVINSRTQGFLALFSGDTGEIRSEIRDQINTKVAEWKEEGKAEIVPGVLFIDEV
HMLDIECFSYINRALESDLAPIVIMASNRGVSRIRGTDYKSPHGLPLDFLDRVVIINTHP
YTPDELRQILSIRAQEEEVDLTPDALALLTKIGQEAGLRYASNLITTSQLIAAKRRAKQV
GVEDVQRSFKLFYDPARSVRFVQESEKRLIGNDGVVDFSYQGAAEAAAPTLPAAAPVDPV
GGEKMDMS

Sequence of entity 3 (G), FASTA

>8OOR_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

>8OOR_4 Ino eighty subunit 2 (chains H)
MSTRPRRHAAQRASQAITDLADRDRESDHSHGPISSRMSSFNSSSRSRLPGKGIASVSRS
EAGGASDPEHIHLTVKLPSSKLRQATSSSGIKKAGSVGSSSSSSGGGKAAVKRARGGKRS
RVLESSEEEEEENEVEVLGDEDEEEEEEEDEIEVREGEGYDEDEEDVEDEDEEMQDLGEE
DADGEDDEMDVDAEGEEDADGDVNMDAGVVGARATTVRAVPPAIKVTKPPKESPSNGKAA
TASKANDNAVPVKRPAPDSDDESLSSLESEPEEEVNVAGGEDAEGEDDDAEGEVDAEGEE
EEEEEEIEVADEDAEGEDVEQDEDEDEEEEDDDDEMISRAQTPDMSRLTARQRARLGEAS
GEYLKLSDEVQSKKHFTAEELSMRRAEMARRRRNLSEKRNEEIKMETVNKLLKKQAPRTT
RRAAQAAAAAEEAEEAAKQPKRPDPMMIRWVNNKMGSVVAVPEELLGTHAGVVFGAGPGK
GLPAGKMVEEVS

Sequence of entity 5 (I), FASTA

>8OOR_5 Chromatin-remodeling complex subunit IES6 (chains I)
MSNPDAQSAQAAHQALVEQLDLHSIHKTFRNPNWRPNQRRNKTIKAILGESQRKEASSTS
AVATPRADDNGGGSGADTPANNDNNDGLSTSGTSTPANGNGSGAGTPASNGQPNLAQASR
SLQKLVLEKSLASAQAPDKKAANGFASSAPTATYTNIESAPSLAPMKHYCDVTGLPAPYL
DPKTRLRYHNKEIFAMIRNLPQGMGEQFLEARGAHTVLK

Sequence of entity 6 (J), FASTA

>8OOR_6 Actin-related protein 5 (chains J)
MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIV
IDNGSHSVRAGWNFEDKPRLAIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFE
AGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTEAVANLPYSRKSMSEIIFECY
GAPSLVYGIDSLFSFRHNQGQTGLVVSSSYSATHVIPVYNRKALLSQAIRLNWGGWHMAE
YMLKLLKLKYYTGFPGKLNSSQTEHMVRDFCYVSLDYDRELAGYLDWTGLEDRERIVQYP
YTEEVVVQKTEEELARIAERKKESGRRLQEQAAKMRLERLMKKEQELEYYKDIQRRMQGE
SKKEIKRLLDEAELKDEAALERVIRDLERSIKRARQKDLGEPEEEEVPDFSLLDVPDDQL
DEAGLRQKRQQRLLKSNWEARQRAKAEKEAEKARLAEEARLDEERRKNDLEGWLEEKRQL
RLAKLNQLKERERLKADLGNRKSLASQIRMKNIANLASDNPTGSGSRKRRRGGAGADQDD
DFGADDADWGVYRSVAIGANKGDDSDDEEGEEDLEAAIRSLENDLLRYDKTFSYDMTLDA
QRDWSKSLLHAFRYGPRPFDPSSQAETHRVHLNVERIRVPEVLFQPAAIAGVDQAGLVEI
AGDILCQRLPSLPGIQDAPDAFLRDVFLTGGNTLFQNFDERLRQGLMALLPVGAPLRVRR
AQDAILDAWRGAAGWACTEEAKAAWITREEYLEKGGEYIKEHDLGNAFA

Ligands and cofactors

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

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
5FM7 2.9 Å, Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(ADP)
8OOC 2.93 Å, CryoEM Structure INO80core Hexasome complex Rvb core refinement state1
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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