8EUF: Class2 of the INO80-Nucleosome complex

Class2 of the INO80-Nucleosome complex. Determined by electron microscopy at 3.41 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 3.41 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 10
Atoms: 28,707
Mol. weight: 619.88 kDa
Ligands: ADP
Released: 12 Jul 2023

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

Secondary structure: helices and β-sheets

8EUF contains 183 α-helices and 208 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	950-951	2	1
β-strand	954	1	2
α-helix	958-971	14
α-helix	975-984	10
α-helix	1000-1012	13
α-helix	1014-1017	4
β-strand	1023	1	3
β-strand	1026-1027	2	4
β-strand	1030	1	5
β-strand	1071-1073	3	6
β-strand	1078	1	5
β-strand	1082-1084	3	7
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	8
α-helix	1139-1144	6
α-helix	1148-1153	6
α-helix	1170-1177	8
α-helix	1186-1189	4
α-helix	1194-1200	7
α-helix	1203-1205	3
α-helix	1206-1208	3
β-strand	1214-1215	2	4
α-helix	1217-1219	3
β-strand	1220-1222	3	7
α-helix	1227-1237	11
α-helix	1240-1245	6
α-helix	1251-1255	5
α-helix	1256-1260	5
α-helix	1269-1270	2
α-helix	1275-1277	3
β-strand	1287	1	3
α-helix	1291-1297	7
α-helix	1299-1310	12
β-strand	1317-1318	2	1
β-strand	1321	1	9
α-helix	1326-1334	9
α-helix	1357-1362	6
β-strand	1373	1	9
β-strand	1389-1391	3	1
α-helix	1398-1404	7
β-strand	1420-1421	2	1
β-strand	1424	1	2
α-helix	1428-1434	7

Chain R: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	40-43	4	10
β-strand	49-52	4	10
β-strand	61-63	3	10
β-strand	67	1	11
β-strand	70	1	12
β-strand	79	1	12
β-strand	82	1	11
α-helix	90-94	5
β-strand	97	1	11
α-helix	108-121	14
α-helix	124-126	3
β-strand	134-137	4	10
α-helix	144-151	8
α-helix	152-156	5
α-helix	157-158	2
β-strand	163-166	4	10
α-helix	168-176	9
β-strand	184-189	6	13
β-strand	194-200	7	13
β-strand	203-204	2	13
β-strand	210-212	3	13
α-helix	217-230	14
α-helix	240-249	10
α-helix	257-263	7
α-helix	270-273	4
β-strand	277-278	2	14
α-helix	279-280	2
α-helix	590-596	7
α-helix	606-609	4
β-strand	611-612	2	14
α-helix	620-623	4
α-helix	628-631	4
α-helix	638-648	11
β-strand	653	1	15
β-strand	656	1	15
α-helix	659-666	8
β-strand	668-671	4	13
α-helix	673-676	4
α-helix	680-691	12
β-strand	693	1	16
β-strand	700-701	2	13
α-helix	709-719	11
α-helix	721-727	7
α-helix	731-737	7

Chain S: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	29-38	10
α-helix	63-82	20
β-strand	104	1	13
α-helix	105-108	4
α-helix	111-114	4
β-strand	115	1	17
β-strand	122	1	17
β-strand	125-126	2	18
β-strand	133-134	2	18
α-helix	137-139	3
α-helix	140-144	5
α-helix	147-148	2
α-helix	152-158	7

Chain T: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	19
β-strand	35	1	20
β-strand	41	1	20
β-strand	44-45	2	21
β-strand	48-49	2	21
α-helix	52-67	16
β-strand	70	1	22
β-strand	74-79	6	23
α-helix	85-96	12
β-strand	102-106	5	23
α-helix	107-110	4
α-helix	117-127	11
β-strand	129-143	15	24
β-strand	146-150	5	16
β-strand	165-171	7	16
β-strand	176-181	6	16
α-helix	183-191	9
β-strand	198-203	6	24
β-strand	209-214	6	24
β-strand	224	1	25
β-strand	229	1	24
α-helix	230-233	4
β-strand	238-248	11	24
α-helix	249-255	7
α-helix	274-277	4
α-helix	282-297	16
β-strand	301-305	5	24
β-strand	307-311	5	23
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-340	6	23
β-strand	342	1	26
β-strand	344-346	3	27
α-helix	347	1
β-strand	354-356	3	27
α-helix	363-365	3
β-strand	369-372	4	23
α-helix	377-390	14
β-strand	394-395	2	28
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-428	10
β-strand	433-434	2	28
α-helix	436-445	10
β-strand	447	1	29
α-helix	449-458	10

Chain U: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	30
β-strand	31	1	31
β-strand	37	1	31
β-strand	40-41	2	32
β-strand	44-45	2	32
α-helix	48-63	16
β-strand	66	1	19
β-strand	70-74	5	29
α-helix	81-92	12
β-strand	98-102	5	29
α-helix	103-105	3
α-helix	113-122	10
β-strand	126-146	21	25
β-strand	155-161	7	25
β-strand	166-171	6	25
α-helix	173-180	8
β-strand	188-193	6	25
β-strand	198-204	7	25
β-strand	221	1	25
α-helix	223-226	4
β-strand	231-240	10	25
α-helix	241-248	8
α-helix	256-259	4
α-helix	267-283	17
β-strand	287-289	3	25
β-strand	292-296	5	29
α-helix	298-300	3
β-strand	302	1	33
α-helix	303-312	10
β-strand	320-325	6	29
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	351-355	5	29
α-helix	356	1
α-helix	361-374	14
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	431	1	36
α-helix	433-442	10
β-strand	448	1	37

Chain V: 21 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	30
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	6
β-strand	163-171	9	6
β-strand	177-181	5	6
α-helix	183-191	9
β-strand	198-203	6	6
β-strand	209-215	7	6
β-strand	223	1	41
β-strand	229-230	2	6
α-helix	232-233	2
β-strand	239-248	10	6
α-helix	249-257	9
α-helix	265-272	8
α-helix	274-275	2
α-helix	282-297	16
β-strand	301-304	4	6
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	42
α-helix	347	1
β-strand	354-356	3	42
α-helix	361-366	6
β-strand	369-371	3	36
α-helix	377-390	14
β-strand	394-395	2	43
α-helix	397-409	13
α-helix	412-416	5
α-helix	419-428	10
β-strand	433-434	2	43
α-helix	436-445	10
β-strand	447	1	44
α-helix	449-457	9

Chain W: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	45
β-strand	31	1	46
β-strand	37	1	46
β-strand	40-41	2	47
β-strand	44-45	2	47
α-helix	48-63	16
β-strand	66	1	38
β-strand	70-74	5	44
α-helix	81-91	11
β-strand	98-102	5	44
α-helix	103-105	3
α-helix	113-124	12
β-strand	126-147	22	41
β-strand	154-161	8	41
β-strand	166-171	6	41
α-helix	173-180	8
β-strand	188-193	6	41
β-strand	198-204	7	41
α-helix	219-220	2
β-strand	221	1	41
α-helix	223-225	3
β-strand	230-240	11	41
α-helix	241-249	9
α-helix	253-259	7
α-helix	267-282	16
β-strand	286-289	4	41
β-strand	292-296	5	44
α-helix	298-300	3
α-helix	303-312	10
β-strand	320-325	6	44
β-strand	330-331	2	48
α-helix	332	1
β-strand	338-339	2	48
α-helix	340-342	3
α-helix	345-349	5
β-strand	351-355	5	44
α-helix	361-374	14
β-strand	379	1	49
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	49
α-helix	420-429	10
β-strand	431	1	50
α-helix	433-442	10
β-strand	448	1	51

Chain X: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	52
β-strand	35	1	53
α-helix	36	1
α-helix	40	1
β-strand	41	1	53
α-helix	42	1
β-strand	44-45	2	54
β-strand	48-49	2	54
α-helix	52-67	16
β-strand	70	1	45
β-strand	74-78	5	50
α-helix	85-96	12
β-strand	102-106	5	50
α-helix	107-110	4
α-helix	117-127	11
β-strand	130-151	22	41
α-helix	152	1
β-strand	162-172	11	41
β-strand	175-180	6	41
α-helix	186-191	6
β-strand	198-203	6	41
β-strand	213-215	3	41
β-strand	224	1	8
β-strand	229-230	2	41
α-helix	231-234	4
β-strand	238-248	11	41
α-helix	249-257	9
α-helix	265-272	8
α-helix	282-297	16
β-strand	301-304	4	41
β-strand	307-311	5	50
α-helix	313-315	3
β-strand	317	1	55
α-helix	318-328	11
β-strand	336-340	5	50
β-strand	342	1	51
β-strand	344-346	3	56
α-helix	347	1
β-strand	348	1	55
β-strand	354-356	3	56
α-helix	361-366	6
β-strand	368-371	4	50
α-helix	377-391	15
β-strand	394-395	2	57
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-427	9
β-strand	433-434	2	57
α-helix	436-445	10
β-strand	447	1	58
α-helix	449-458	10

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	1489	Saccharomyces cerevisiae S288C	P53115 (AlphaFold model)
Actin-related protein 5	R	protein	755	Saccharomyces cerevisiae S288C	P53946 (AlphaFold model)
Chromatin-remodeling complex subunit IES6	S	protein	166	Saccharomyces cerevisiae S288C	P32617 (AlphaFold model)
RuvB-like protein 1	T, V, X	protein	463	Saccharomyces cerevisiae S288C	Q03940 (AlphaFold model)
RuvB-like protein 2	U, W, Y	protein	460	Saccharomyces cerevisiae S288C	Q12464
Ino eighty subunit 2	Z	protein	320	Saccharomyces cerevisiae S288C	P40154

Sequence of entity 1 (Q), FASTA

>8EUF_1 Chromatin-remodeling ATPase INO80 (chains Q)
MSLAVLLNKEDKDISDFSKTTAGKSAKKNSRERVADVAPTRVLDKKQAYLSQLNSEFNRI
KRRDSIEQLYQDWKFINLQEFELISEWNQQSKDWQFDNTNDSQDLHFKKLYRDMSMINKE
WAEYQSFKNANLSDIINEKDADEDEEDDEDELEDGEEDMEEDEASTGRHTNGKSMRGNGI
QKSRKKDAAAAAAIGKAIKDDQTHADTVVTVNGDENEDGNNGEDEDNDNDNENNNDNDND
NENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDFNPDVEKRRKRS
SSSSSSTKLSMNSLSLITSKKINKNITINSDRPKIVRELIKMCNKNKHQKIKKRRFTNCI
VTDYNPIDSKLNIKITLKQYHVKRLKKLINDAKREREREEALKNNVGLDGNDLDNDEDGS
ESHKRRKLNNNTANGADDANKRKFNTRHGLPTYGMKMNAKEARAIQRHYDNTYTTIWKDM
ARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMS
NFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKIK
TNELEGNNVSSNDSESQKNIDISALAPNKNDFHAIDFDNENDEQLRLRAAENASNALAET
RAKAKQFDDHANAHEEEEEEDELNFQNPTSLGEITIEQPKILACTLKEYQLKGLNWLANL
YDQGINGILADEMGLGKTVQSISVLAHLAENHNIWGPFLVVTPASTLHNWVNEISKFLPQ
FKILPYWGNANDRKVLRKFWDRKNLRYNKNAPFHVMVTSYQMVVTDANYLQKMKWQYMIL
DEAQAIKSSQSSRWKNLLSFHCRNRLLLTGTPIQNSMQELWALLHFIMPSLFDSHDEFNE
WFSKDIESHAEANTKLNQQQLRRLHMILKPFMLRRVKKNVQSELGDKIEIDVLCDLTQRQ
AKLYQVLKSQISTNYDAIENAATNDSTSNSASNSGSDQNLINAVMQFRKVCNHPDLFERA
DVDSPFSFTTFGKTTSMLTASVANNNSSVISNSNMNLSSMSSNNISNGKFTDLIYSSRNP
IKYSLPRLIYEDLILPNYNNDVDIANKLKNVKFNIFNPSTNYELCLFLSKLTGEPSLNEF
FRVSTTPLLKRVIERTNGPKNTDSLSFKTITQELLEVTRNAPSEGVMASLLNVEKHAYER
EYLNCIQRGYHPNVSAPPVTIEVLGSSHVTNSINNELFDPLISQALSDIPAITQYNMHVK
KGIPVEDFPKTGLFPEPLNKNFSSNISMPSMDRFITESAKLRKLDELLVKLKSEGHRVLI
YFQMTKMMDLMEEYLTYRQYNHIRLDGSSKLEDRRDLVHDWQTNPEIFVFLLSTRAGGLG
INLTAADTVIFYDSDWNPTIDSQAMDRAHRLGQTRQVTVYRLLVRGTIEERMRDRAKQKE
QVQQVVMEGKTQEKNIKTIEVGENDSEVTREGSKSISQDGIKEAASALA

Sequence of entity 2 (R), FASTA

>8EUF_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

>8EUF_3 Chromatin-remodeling complex subunit IES6 (chains S)
MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRH
KSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTG
LKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK

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

>8EUF_4 RuvB-like protein 1 (chains T, V, X)
MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGV
IVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTET
LMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLR
LDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK
KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGV
AELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVP
PDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLA
PCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYL

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

>8EUF_5 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK

Sequence of entity 6 (Z), FASTA

>8EUF_6 Ino eighty subunit 2 (chains Z)
MDSEASDIEAELSDSVSAGGEEYIDDDDYTEDIDDQIVTAKSSRRTARRSVPKGVRTSKR
IRDKELSVEVDEDYDEEEDVLSPSKKRHLHTRSMDKRQVAATASEKSDIGDSKGNDGEIE
DGILEEEESLEKELNRGGGKEVEKSEESYYAQNDVGQKGEEEQDGESGGYEDNEPSISKE
SDELVSVVNGNGNEEDDEVEATKENTTDSTRSTTTRSKMLLDLLEDGGSKKKLTDEEIQL
RRAENARKRKNLSEKRLEEEKQDTINKLLKKRAGKSRSHLPNDDEKNDGSSSFVKPRRPY
NSEGMTRILRRYEEDLFCTF

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

Browse structure collections

About this viewer

MolViewer shows 8EUF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.