8ETU: Class2 of the INO80-Hexasome complex

Class2 of the INO80-Hexasome complex. Determined by electron microscopy at 2.8 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 10
Atoms: 28,670
Mol. weight: 459.58 kDa
Ligands: ADP
Released: 19 Jul 2023

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

Secondary structure: helices and β-sheets

8ETU contains 188 α-helices and 195 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 Q: 29 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	949-954	6	53
α-helix	958-970	13
α-helix	975-984	10
α-helix	1000-1012	13
α-helix	1014-1017	4
β-strand	1023	1	54
β-strand	1026-1027	2	55
β-strand	1071-1073	3	29
β-strand	1082-1084	3	56
α-helix	1087-1089	3
α-helix	1090-1094	5
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1122-1132	11
β-strand	1136	1	51
α-helix	1139-1143	5
α-helix	1148-1153	6
α-helix	1170-1175	6
α-helix	1177-1179	3
α-helix	1186-1190	5
α-helix	1193-1200	8
β-strand	1214-1215	2	55
β-strand	1216	1	30
α-helix	1217-1219	3
β-strand	1220-1222	3	56
α-helix	1227-1237	11
α-helix	1240-1245	6
α-helix	1251-1258	8
α-helix	1265-1267	3
α-helix	1269-1270	2
α-helix	1275-1277	3
α-helix	1281-1283	3
β-strand	1287	1	54
α-helix	1293-1297	5
α-helix	1299-1314	16
β-strand	1318-1322	5	53
α-helix	1326-1338	13
β-strand	1342	1	53
α-helix	1357-1363	7
β-strand	1369-1373	5	53
β-strand	1388-1391	4	53
α-helix	1398-1407	10
β-strand	1418-1424	7	53
α-helix	1428-1431	4

Chain R: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	1
α-helix	18-22	5
α-helix	25-27	3
α-helix	31-33	3
β-strand	40-44	5	2
β-strand	48-53	6	2
β-strand	61-64	4	2
β-strand	67-71	5	3
α-helix	72	1
β-strand	78-82	5	3
α-helix	83-86	4
α-helix	90-94	5
β-strand	97	1	3
β-strand	100-101	2	4
β-strand	104-105	2	4
α-helix	109-121	13
β-strand	134-135	2	2
α-helix	144-151	8
α-helix	152-158	7
β-strand	162-163	2	5
α-helix	168-176	9
β-strand	184-189	6	6
β-strand	194-200	7	6
β-strand	203-204	2	6
β-strand	210-212	3	6
α-helix	216-230	15
α-helix	240-249	10
α-helix	257-261	5
β-strand	275-278	4	1
α-helix	586-588	3
α-helix	590-596	7
α-helix	608-610	3
β-strand	611-614	4	1
α-helix	617-620	4
α-helix	622-625	4
α-helix	628-630	3
α-helix	638-648	11
β-strand	653	1	7
β-strand	656	1	7
α-helix	659-665	7
β-strand	668-671	4	6
α-helix	673-675	3
α-helix	680-691	12
β-strand	693	1	8
β-strand	700-702	3	6
α-helix	709-719	11
α-helix	721-724	4
β-strand	729-730	2	5
α-helix	731-737	7

Chain S: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	32-37	6
α-helix	55-57	3
α-helix	63-82	20
β-strand	104	1	6
α-helix	105-108	4
α-helix	111-114	4
β-strand	115	1	9
β-strand	122	1	9
β-strand	125-126	2	10
β-strand	133-134	2	10
α-helix	137-139	3
α-helix	140-144	5
α-helix	147-148	2
α-helix	152-158	7

Chain T: 20 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	11
β-strand	35	1	12
β-strand	41	1	12
β-strand	45	1	13
β-strand	48	1	13
α-helix	52-67	16
β-strand	70	1	14
β-strand	74-78	5	15
α-helix	85-96	12
β-strand	102-106	5	15
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-151	23	8
β-strand	163-172	10	8
β-strand	175-181	7	8
α-helix	183-191	9
β-strand	198-203	6	8
β-strand	209-215	7	8
α-helix	216-218	3
β-strand	224	1	16
β-strand	229-230	2	8
α-helix	231-233	3
β-strand	238-248	11	8
α-helix	249-255	7
α-helix	270-271	2
α-helix	282-297	16
β-strand	301-305	5	8
β-strand	307-311	5	15
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-340	6	15
β-strand	342	1	17
β-strand	344-346	3	18
α-helix	347	1
β-strand	354-356	3	18
α-helix	361-364	4
β-strand	367-371	5	15
α-helix	373-375	3
α-helix	377-390	14
β-strand	394-395	2	19
α-helix	397-409	13
α-helix	412-428	17
β-strand	433-434	2	19
α-helix	436-445	10
β-strand	447	1	20
α-helix	449-457	9

Chain U: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	21
β-strand	37	1	21
β-strand	40-41	2	22
β-strand	44-45	2	22
α-helix	48-63	16
β-strand	66	1	11
β-strand	70-74	5	20
α-helix	81-92	12
β-strand	98-102	5	20
α-helix	113-122	10
β-strand	125-147	23	16
β-strand	154-161	8	16
β-strand	166-171	6	16
α-helix	173-180	8
β-strand	188-193	6	16
β-strand	199-204	6	16
β-strand	221	1	16
α-helix	223-225	3
β-strand	230-240	11	16
α-helix	241-248	8
α-helix	256-259	4
α-helix	267-283	17
β-strand	287-290	4	16
β-strand	292-296	5	20
α-helix	298-300	3
α-helix	303-312	10
β-strand	320-325	6	20
β-strand	329-331	3	23
α-helix	332	1
β-strand	338-340	3	23
α-helix	345-348	4
β-strand	351-355	5	20
α-helix	361-374	14
β-strand	379	1	24
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	24
α-helix	420-429	10
β-strand	431	1	25
α-helix	433-441	9

Chain V: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	26
β-strand	35	1	27
α-helix	40	1
β-strand	41	1	27
α-helix	42	1
β-strand	44-45	2	28
β-strand	48-49	2	28
α-helix	52-67	16
β-strand	74-78	5	25
α-helix	86-96	11
β-strand	102-106	5	25
α-helix	107-110	4
α-helix	117-127	11
β-strand	129-151	23	29
β-strand	163-172	10	29
β-strand	175-181	7	29
α-helix	183-191	9
β-strand	198-203	6	29
β-strand	209-215	7	29
β-strand	229-230	2	29
α-helix	232-233	2
β-strand	238-248	11	29
α-helix	249-257	9
β-strand	261	1	30
α-helix	265-272	8
α-helix	274-275	2
α-helix	282-297	16
β-strand	301-305	5	29
β-strand	307-311	5	25
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-340	6	25
β-strand	344-346	3	31
α-helix	347	1
β-strand	354-356	3	31
α-helix	361-364	4
β-strand	368-371	4	25
α-helix	377-390	14
β-strand	395	1	32
α-helix	397-409	13
α-helix	412-416	5
α-helix	419-427	9
β-strand	434	1	32
α-helix	436-445	10
β-strand	447	1	33
α-helix	449-457	9

Chain W: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	34
β-strand	31	1	35
β-strand	37	1	35
β-strand	40-41	2	36
β-strand	44-45	2	36
α-helix	48-63	16
β-strand	66	1	26
β-strand	70-74	5	33
α-helix	81-92	12
β-strand	98-102	5	33
α-helix	103-105	3
α-helix	113-122	10
β-strand	125-147	23	37
β-strand	154-161	8	37
β-strand	166-171	6	37
α-helix	173-180	8
β-strand	188-193	6	37
β-strand	198-204	7	37
β-strand	221	1	37
α-helix	223-225	3
β-strand	230-240	11	37
α-helix	241-249	9
α-helix	253-259	7
α-helix	267-283	17
β-strand	286-290	5	37
β-strand	292-296	5	33
α-helix	303-312	10
α-helix	319	1
β-strand	320-325	6	33
β-strand	330-331	2	38
α-helix	332	1
β-strand	338-339	2	38
α-helix	340-342	3
α-helix	345-349	5
β-strand	351-355	5	33
α-helix	361-374	14
β-strand	379	1	39
α-helix	381-393	13
α-helix	396-410	15
α-helix	411-413	3
β-strand	418	1	39
α-helix	420-429	10
β-strand	431	1	40
α-helix	433-441	9
β-strand	448	1	41
α-helix	449	1

Chain X: 25 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	42
α-helix	40-42	3
β-strand	44-45	2	43
β-strand	48-49	2	43
α-helix	52-67	16
β-strand	70	1	34
β-strand	74-78	5	40
α-helix	85-96	12
β-strand	102-106	5	40
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-151	23	44
α-helix	152	1
α-helix	155-156	2
β-strand	160-172	13	44
β-strand	175-181	7	44
α-helix	183-185	3
α-helix	186-192	7
β-strand	198-203	6	44
β-strand	210-215	6	44
α-helix	216-218	3
β-strand	229-230	2	44
α-helix	231-234	4
β-strand	238-248	11	44
α-helix	249-257	9
α-helix	259-260	2
α-helix	265-271	7
α-helix	282-297	16
β-strand	301-305	5	44
β-strand	307-311	5	40
α-helix	313-315	3
β-strand	317	1	45
α-helix	318-327	10
β-strand	335-340	6	40
β-strand	342	1	41
β-strand	344-346	3	46
α-helix	347	1
β-strand	348	1	45
β-strand	354-356	3	46
α-helix	361-364	4
β-strand	367-371	5	40
α-helix	377-390	14
β-strand	394-395	2	47
α-helix	397-409	13
α-helix	412-417	6
α-helix	420-428	9
β-strand	433-434	2	47
α-helix	436-445	10
β-strand	447	1	48
α-helix	449-457	9

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
Actin-related protein 5	R	protein	744	Saccharomyces cerevisiae S288C	P53946 (AlphaFold model)
Chromatin-remodeling complex subunit IES6	S	protein	139	Saccharomyces cerevisiae S288C	P32617 (AlphaFold model)
RuvB-like protein 1	T, V, X	protein	443	Saccharomyces cerevisiae S288C	Q03940 (AlphaFold model)
RuvB-like protein 2	U, W, Y	protein	457	Saccharomyces cerevisiae S288C	Q12464 (AlphaFold model)
Chromatin-remodeling ATPase INO80	Q	protein	485	Saccharomyces cerevisiae S288C	P53115
Ino eighty subunit 2	Z	protein	28	Saccharomyces cerevisiae S288C	P40154

Sequence of entity 1 (R), FASTA

>8ETU_1 Actin-related protein 5 (chains R)
KAVVIDDPPLRQTPEPFDEQSAYNPQSPIAIDFGSSKLRAGFVNHATPTHIFPNALTKFR
DRKLNKNFTFVGNDTLLDQAVRSQSRSPFDGPFVTNWNLTEEILDYTFHHLGVVPDNGIP
NPILLTERLATVQSQRTNWYQILFETYNVPGVTFGIDSLFSFYNYNPSGNKTGLVISCGH
EDTNVIPVVDGAGILTDAKRINWGGHQAVDYLNDLMALKYPYFPTKMSYLQYETMYKDYC
YVSRNYDEDIEKILTLENLDTNDVVVEAPFTEVLQPQKTEEELRIQAEKRKETGKRLQEQ
ARLKRMEKLVQKQEEFEYFSKVRDQLIDEPKKKVLSVLQNAGFDDERDFKKYLHSLEQSL
KKAQMVEAEDDSHLDEMNEDKTAQKFDLLDIADEDLNEDQIKEKRKQRFLKASQDARQKA
KEEKERVAKEEEEKKLKEQQWRETDLNGWIKDKRLKLNKLIKRRKEKLKLRDEMKDRKSQ
VSQNRMKNLASLAEDNVKQGAKRNRHQATIDNDPNDTFGANDEDWLIYTDITQNPEAFEE
ALEYEYKDIVELERLLLEHDPNFTEEDTLEAQYDWRNSILHLFLRGPRPHDSENIHEQHQ
MHLNVERIRVPEVIFQPTMGGQDQAGICELSETILLKKFGSQPGKLSQTSIDMVNNVLIT
GGNAKVPGLKERIVKEFTGFLPTGTNITVNMSSDPSLDAWKGMAALARNEEQYRKTVISK
KEYEEYGPEYIKEHKLGNTKYFED

Sequence of entity 2 (S), FASTA

>8ETU_2 Chromatin-remodeling complex subunit IES6 (chains S)
ERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRHKSARQLISDENKRINALLTKANKAAES
STAARRLVPKATYFSVEAPPSIRPAKKYCDVTGLKGFYKSPTNNIRYHNAEIYQLIVKPM
APGVDQEYLKLRGANFVLK

Sequence of entity 3 (T, V, X), FASTA

>8ETU_3 RuvB-like protein 1 (chains T, V, X)
VTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGVIVDLIKAKKMSGRAILLAGG
PSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTETLMENFRRAIGLRIKETKEVY
EGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLRLDPTIYESIQREKVSIGDVI
YIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKKKEIVQDVTLHDLDVANARPQ
GGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGVAELIPGVLFIDEVNMLDIEI
FTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVPPDLIDRLLIVRTLPYDKDEI
RTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLAPCGILAQTSNRKEIVVNDVN
EAKLLFLDAKRSTKILETSANYL

Sequence of entity 4 (U, W, Y), FASTA

>8ETU_4 RuvB-like protein 2 (chains U, W, Y)
KSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKMVQNGTIAGRAVLVA
GPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQAFRKSIGIKIKEETE
LIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLTKEKVLAGDVISIDK
ASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVSLHEIDVINSRTQGF
LALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSFINRALE
DEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYNEQEIKTILSIRAQE
EEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEVEDVKRAYLLFLDSA
RSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE

Sequence of entity 5 (Q), FASTA

>8ETU_5 Chromatin-remodeling ATPase INO80 (chains Q)
IEIDVLCDLTQRQAKLYQVLKSQISTNYDAIENAATNDSTSNSASNSGSDQNLINAVMQF
RKVCNHPDLFERADVDSPFSFTTFGKTTSMLTASVANNNSSVISNSNMNLSSMSSNNISN
GKFTDLIYSSRNPIKYSLPRLIYEDLILPNYNNDVDIANKLKNVKFNIFNPSTNYELCLF
LSKLTGEPSLNEFFRVSTTPLLKRVIERTNGPKNTDSLSFKTITQELLEVTRNAPSEGVM
ASLLNVEKHAYEREYLNCIQRGYHPNVSAPPVTIEVLGSSHVTNSINNELFDPLISQALS
DIPAITQYNMHVKKGIPVEDFPKTGLFPEPLNKNFSSNISMPSMDRFITESAKLRKLDEL
LVKLKSEGHRVLIYFQMTKMMDLMEEYLTYRQYNHIRLDGSSKLEDRRDLVHDWQTNPEI
FVFLLSTRAGGLGINLTAADTVIFYDSDWNPTIDSQAMDRAHRLGQTRQVTVYRLLVRGT
IEERM

Sequence of entity 6 (Z), FASTA

>8ETU_6 Ino eighty subunit 2 (chains Z)
FVKPRRPYNSEGMTRILRRYEEDLFCTF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6

Primary citation

Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Wu, H., Munoz, E.N., Hsieh, L.J. et al. Science (2023) 381:319-324. DOI 10.1126/science.adf4197 · PubMed

Other PDB entries of the same protein (UniProt P53946 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9C9Z 2.55 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, INO80 Core
8ETW 2.64 Å, Class3 of INO80-Hexasome complex
9CAT 2.9 Å, DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module
9C9G 2.91 Å, S.c INO80 in complex with S.c 0/80 nucleosome
9CCD 3.01 Å, DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module
8ETS 3.04 Å, Class1 of the INO80-Hexasome complex
9C9S 3.09 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 1
9C9T 3.16 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 2
9OB1 3.2 Å, S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State
9CAN 3.3 Å, S.c INO80 in complex with Xenopus 0/40 nucleosome
8EUF 3.41 Å, Class2 of the INO80-Nucleosome complex
8EU9 3.48 Å, Class1 of the INO80-Nucleosome complex

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