8EU9: Class1 of the INO80-Nucleosome complex

Class1 of the INO80-Nucleosome complex. Determined by electron microscopy at 3.48 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 3.48 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288C
Chains: 10
Atoms: 28,517
Mol. weight: 457.86 kDa
Ligands: ADP
Released: 12 Jul 2023

Explore 8EU9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EU9 contains 203 α-helices and 212 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: 33 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	949-954	6	1
α-helix	955-957	3
α-helix	958-969	12
α-helix	977-981	5
α-helix	982-984	3
α-helix	1000-1012	13
β-strand	1023	1	2
β-strand	1026-1027	2	3
β-strand	1071-1072	2	4
β-strand	1082-1085	4	5
α-helix	1087-1089	3
α-helix	1090-1094	5
α-helix	1102-1110	9
α-helix	1122-1132	11
β-strand	1136	1	6
α-helix	1139-1144	6
α-helix	1148-1153	6
α-helix	1170-1177	8
α-helix	1186-1190	5
α-helix	1194-1200	7
α-helix	1203-1205	3
β-strand	1214-1215	2	3
β-strand	1216	1	7
α-helix	1217-1219	3
β-strand	1220-1223	4	5
α-helix	1228-1237	10
α-helix	1240-1245	6
α-helix	1251-1255	5
α-helix	1256-1260	5
α-helix	1265-1267	3
α-helix	1269-1270	2
α-helix	1275-1277	3
α-helix	1280-1282	3
β-strand	1287	1	2
α-helix	1288-1290	3
α-helix	1291-1296	6
α-helix	1301-1310	10
β-strand	1317-1319	3	8
α-helix	1320-1322	3
α-helix	1328-1336	9
β-strand	1342	1	9
α-helix	1357-1363	7
β-strand	1368	1	9
β-strand	1370-1372	3	8
β-strand	1390	1	8
α-helix	1398-1407	10
β-strand	1419-1424	6	1
α-helix	1428-1432	5
α-helix	1435-1439	5

Chain R: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	10
α-helix	25-28	4
β-strand	40-43	4	11
β-strand	50-53	4	11
β-strand	61-62	2	11
β-strand	67	1	12
β-strand	69	1	13
α-helix	71-72	2
β-strand	80	1	13
α-helix	84-87	4
α-helix	90-95	6
β-strand	97	1	12
β-strand	100	1	14
β-strand	105	1	14
α-helix	108-122	15
α-helix	124-126	3
β-strand	134-135	2	11
β-strand	136-138	3	15
α-helix	139	1
α-helix	144-151	8
α-helix	152-156	5
β-strand	163	1	16
β-strand	165-167	3	15
α-helix	168-176	9
β-strand	184-189	6	17
β-strand	194-200	7	17
β-strand	203-204	2	17
β-strand	210-212	3	17
α-helix	216-230	15
α-helix	240-249	10
α-helix	257-260	4
α-helix	275	1
β-strand	276-278	3	10
α-helix	590-596	7
α-helix	600-601	2
α-helix	606-610	5
β-strand	611-613	3	10
α-helix	622-624	3
α-helix	628-631	4
α-helix	638-643	6
α-helix	644-648	5
α-helix	659-666	8
β-strand	668-671	4	17
α-helix	680-691	12
β-strand	693	1	18
β-strand	700-702	3	17
α-helix	709-719	11
α-helix	721-727	7
β-strand	729	1	16
α-helix	731-736	6
α-helix	738-740	3

Chain S: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	30-40	11
α-helix	58-60	3
α-helix	63-82	20
β-strand	104	1	17
α-helix	105-108	4
α-helix	111-114	4
β-strand	125-126	2	19
β-strand	133-134	2	19
α-helix	137-139	3
α-helix	140-144	5
α-helix	147-148	2
α-helix	151-159	9

Chain T: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	22-23	2
β-strand	24	1	20
β-strand	35	1	21
α-helix	40	1
β-strand	41	1	21
α-helix	42	1
β-strand	44-45	2	22
β-strand	48-49	2	22
α-helix	52-67	16
β-strand	70	1	23
β-strand	74-78	5	24
α-helix	85-96	12
β-strand	102-106	5	24
α-helix	107-110	4
α-helix	117-128	12
β-strand	130-150	21	18
β-strand	165-172	8	18
β-strand	175-181	7	18
α-helix	183-190	8
β-strand	198-203	6	18
β-strand	209-215	7	18
α-helix	219-221	3
β-strand	224	1	19
α-helix	227-228	2
β-strand	229-230	2	18
α-helix	231-233	3
β-strand	238-248	11	18
α-helix	249-254	6
α-helix	270-271	2
α-helix	275-277	3
α-helix	279-281	3
α-helix	282-297	16
β-strand	301-304	4	18
β-strand	307-311	5	24
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-339	5	24
β-strand	342	1	25
β-strand	345-346	2	26
α-helix	347	1
β-strand	354-355	2	26
α-helix	356-358	3
α-helix	361-366	6
β-strand	368-371	4	24
α-helix	377-390	14
β-strand	395	1	27
α-helix	397-409	13
α-helix	412-428	17
β-strand	434	1	27
α-helix	436-445	10
β-strand	447	1	28
α-helix	449-458	10

Chain U: 20 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	29
β-strand	31	1	30
α-helix	36	1
β-strand	37	1	30
α-helix	38	1
β-strand	40-41	2	31
β-strand	44-45	2	31
α-helix	48-63	16
β-strand	66	1	20
β-strand	70-74	5	28
α-helix	81-92	12
β-strand	98-102	5	28
α-helix	113-122	10
β-strand	125-133	9	32
β-strand	136-146	11	19
β-strand	155-161	7	19
β-strand	166-171	6	19
α-helix	173-180	8
β-strand	188-193	6	19
β-strand	198-204	7	19
β-strand	221	1	19
α-helix	223-225	3
β-strand	233-240	8	32
α-helix	241-248	8
α-helix	256-259	4
α-helix	267-283	17
β-strand	287-290	4	32
β-strand	292-296	5	28
α-helix	298-300	3
β-strand	302	1	33
α-helix	303-310	8
β-strand	320-325	6	28
β-strand	330-331	2	34
α-helix	332	1
β-strand	333	1	33
β-strand	338-339	2	34
α-helix	340-342	3
α-helix	345-349	5
β-strand	352-355	4	28
α-helix	361-375	15
β-strand	379	1	35
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	35
α-helix	420-429	10
β-strand	430-431	2	36
α-helix	433-442	10
β-strand	448	1	37

Chain V: 22 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	22-23	2
β-strand	24	1	38
β-strand	35	1	39
β-strand	41	1	39
β-strand	44-45	2	40
β-strand	48-49	2	40
α-helix	52-67	16
β-strand	70	1	29
β-strand	74-78	5	36
α-helix	85-96	12
β-strand	102-106	5	36
α-helix	107-110	4
α-helix	117-128	12
β-strand	130-151	22	4
α-helix	155-157	3
β-strand	163-171	9	4
β-strand	176-181	6	4
α-helix	183-191	9
β-strand	198-203	6	4
β-strand	209-215	7	4
β-strand	229-230	2	4
α-helix	232-233	2
β-strand	239-248	10	4
α-helix	249-257	9
β-strand	261	1	7
α-helix	265-272	8
α-helix	274-275	2
α-helix	282-298	17
β-strand	302-304	3	4
β-strand	307-311	5	36
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-340	6	36
β-strand	342	1	37
β-strand	344-346	3	41
α-helix	347	1
β-strand	354-356	3	41
α-helix	361-364	4
β-strand	367-371	5	36
α-helix	377-390	14
β-strand	395	1	42
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-428	10
β-strand	434	1	42
α-helix	436-445	10
β-strand	446-447	2	43
α-helix	449-458	10

Chain W: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	44
β-strand	31	1	45
β-strand	37	1	45
β-strand	40-41	2	46
β-strand	44-45	2	46
α-helix	48-63	16
β-strand	66	1	38
β-strand	70-74	5	43
α-helix	81-91	11
β-strand	98-99	2	43
β-strand	102	1	47
α-helix	104-106	3
α-helix	113-124	12
β-strand	126-143	18	48
β-strand	146-147	2	48
β-strand	154-161	8	48
β-strand	166-171	6	48
α-helix	173-180	8
β-strand	188-193	6	48
β-strand	198-204	7	48
α-helix	218-220	3
β-strand	221	1	48
α-helix	223-225	3
β-strand	231-240	10	48
α-helix	241-249	9
α-helix	256-259	4
α-helix	267-282	16
β-strand	286-289	4	48
β-strand	292-295	4	43
β-strand	296	1	47
α-helix	298-300	3
α-helix	303-312	10
β-strand	320-324	5	43
β-strand	329-331	3	49
α-helix	332	1
β-strand	338-340	3	49
α-helix	345-350	6
β-strand	352-355	4	43
α-helix	361-374	14
β-strand	379	1	50
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	50
α-helix	420-429	10
β-strand	431	1	51
α-helix	433-442	10
α-helix	444-446	3
β-strand	448	1	52
α-helix	449	1

Chain X: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	53
β-strand	35	1	54
α-helix	36	1
α-helix	40	1
β-strand	41	1	54
α-helix	42	1
α-helix	52-67	16
β-strand	70	1	44
β-strand	74-78	5	51
α-helix	85-96	12
β-strand	102-106	5	51
α-helix	107-109	3
α-helix	117-128	12
β-strand	130-133	4	55
β-strand	137-150	14	56
β-strand	161-162	2	48
β-strand	165-172	8	56
β-strand	175-181	7	56
α-helix	185-191	7
β-strand	198-203	6	56
β-strand	210-215	6	56
β-strand	229-230	2	56
α-helix	231-233	3
β-strand	238-241	4	56
β-strand	245-248	4	55
α-helix	249-257	9
α-helix	259-260	2
α-helix	266-272	7
α-helix	274-275	2
α-helix	282-298	17
β-strand	301-304	4	55
β-strand	307-311	5	51
α-helix	313-315	3
α-helix	318-327	10
β-strand	336-340	5	51
β-strand	342	1	52
β-strand	344-346	3	57
α-helix	347	1
β-strand	354-356	3	57
α-helix	361-364	4
β-strand	368-371	4	51
α-helix	377-391	15
β-strand	394-395	2	58
α-helix	397-409	13
α-helix	412-416	5
α-helix	419-428	10
β-strand	433-434	2	58
α-helix	436-445	10
β-strand	447	1	59
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
Chromatin-remodeling ATPase INO80	Q	protein	493	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53115 (AlphaFold model)
Actin-related protein 5	R	protein	755	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53946 (AlphaFold model)
Chromatin-remodeling complex subunit IES6	S	protein	135	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32617 (AlphaFold model)
RuvB-like protein 1	T, V, X	protein	443	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q03940 (AlphaFold model)
RuvB-like protein 2	U, W, Y	protein	446	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12464
Ino eighty subunit 2	Z	protein	28	Saccharomyces cerevisiae S288C	P40154

Sequence of entity 1 (Q), FASTA

>8EU9_1 Chromatin-remodeling ATPase INO80 (chains Q)
IEIDVLCDLTQRQAKLYQVLKSQISTNYDAIENAATNDSTSNSASNSGSDQNLINAVMQF
RKVCNHPDLFERADVDSPFSFTTFGKTTSMLTASVANNNSSVISNSNMNLSSMSSNNISN
GKFTDLIYSSRNPIKYSLPRLIYEDLILPNYNNDVDIANKLKNVKFNIFNPSTNYELCLF
LSKLTGEPSLNEFFRVSTTPLLKRVIERTNGPKNTDSLSFKTITQELLEVTRNAPSEGVM
ASLLNVEKHAYEREYLNCIQRGYHPNVSAPPVTIEVLGSSHVTNSINNELFDPLISQALS
DIPAITQYNMHVKKGIPVEDFPKTGLFPEPLNKNFSSNISMPSMDRFITESAKLRKLDEL
LVKLKSEGHRVLIYFQMTKMMDLMEEYLTYRQYNHIRLDGSSKLEDRRDLVHDWQTNPEI
FVFLLSTRAGGLGINLTAADTVIFYDSDWNPTIDSQAMDRAHRLGQTRQVTVYRLLVRGT
IEERMRDRAKQKE

Sequence of entity 2 (R), FASTA

>8EU9_2 Actin-related protein 5 (chains R)
MSSRDASLTPLKAVVIDDPPLRQTPEPFDEQSAYNPQSPIAIDFGSSKLRAGFVNHATPT
HIFPNALTKFRDRKLNKNFTFVGNDTLLDQAVRSQSRSPFDGPFVTNWNLTEEILDYTFH
HLGVVPDNGIPNPILLTERLATVQSQRTNWYQILFETYNVPGVTFGIDSLFSFYNYNPSG
NKTGLVISCGHEDTNVIPVVDGAGILTDAKRINWGGHQAVDYLNDLMALKYPYFPTKMSY
LQYETMYKDYCYVSRNYDEDIEKILTLENLDTNDVVVEAPFTEVLQPQKTEEELRIQAEK
RKETGKRLQEQARLKRMEKLVQKQEEFEYFSKVRDQLIDEPKKKVLSVLQNAGFDDERDF
KKYLHSLEQSLKKAQMVEAEDDSHLDEMNEDKTAQKFDLLDIADEDLNEDQIKEKRKQRF
LKASQDARQKAKEEKERVAKEEEEKKLKEQQWRETDLNGWIKDKRLKLNKLIKRRKEKLK
LRDEMKDRKSQVSQNRMKNLASLAEDNVKQGAKRNRHQATIDNDPNDTFGANDEDWLIYT
DITQNPEAFEEALEYEYKDIVELERLLLEHDPNFTEEDTLEAQYDWRNSILHLFLRGPRP
HDSENIHEQHQMHLNVERIRVPEVIFQPTMGGQDQAGICELSETILLKKFGSQPGKLSQT
SIDMVNNVLITGGNAKVPGLKERIVKEFTGFLPTGTNITVNMSSDPSLDAWKGMAALARN
EEQYRKTVISKKEYEEYGPEYIKEHKLGNTKYFED

Sequence of entity 3 (S), FASTA

>8EU9_3 Chromatin-remodeling complex subunit IES6 (chains S)
ERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRHKSARQLISDENKRINALLTKANKAAES
STAARRLVPKATYFSVEAPPSIRPAKKYCDVTGLKGFYKSPTNNIRYHNAEIYQLIVKPM
APGVDQEYLKLRGAN

Sequence of entity 4 (T, V, X), FASTA

>8EU9_4 RuvB-like protein 1 (chains T, V, X)
VTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGVIVDLIKAKKMSGRAILLAGG
PSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTETLMENFRRAIGLRIKETKEVY
EGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLRLDPTIYESIQREKVSIGDVI
YIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKKKEIVQDVTLHDLDVANARPQ
GGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGVAELIPGVLFIDEVNMLDIEI
FTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVPPDLIDRLLIVRTLPYDKDEI
RTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLAPCGILAQTSNRKEIVVNDVN
EAKLLFLDAKRSTKILETSANYL

Sequence of entity 5 (U, W, Y), FASTA

>8EU9_5 RuvB-like protein 2 (chains U, W, Y)
KSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKMVQNGTIAGRAVLVA
GPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQAFRKSIGIKIKEETE
LIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLTKEKVLAGDVISIDK
ASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVSLHEIDVINSRTQGF
LALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSFINRALE
DEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYNEQEIKTILSIRAQE
EEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEVEDVKRAYLLFLDSA
RSVKYVQENESQYIDDQGNVQISIAK

Sequence of entity 6 (Z), FASTA

>8EU9_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 P53115 (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
8ETU 2.8 Å, Class2 of the 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
8A5O 3.2 Å, Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80
9OB1 3.2 Å, S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State
8A5A 3.3 Å, Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80

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