5NBN: Arp4-N-actin-Arp8-Ino80HSA module of INO80

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80. Determined by X-ray diffraction at 4.0 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 4.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 8
Atoms: 23,215
Mol. weight: 376.33 kDa
Ligands: LAR, ATP, CA
Released: 22 Aug 2018

Explore 5NBN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NBN contains 168 α-helices and 132 β-strands across 8 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: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	25-30	6	1
β-strand	38-41	4	1
β-strand	43-47	5	2
α-helix	54-55	2
β-strand	56	1	2
α-helix	59-62	4
β-strand	69-73	5	2
β-strand	75-76	2	3
β-strand	79-80	2	3
α-helix	83-96	14
β-strand	108-112	5	1
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	1
α-helix	142-150	9
β-strand	155-160	6	4
β-strand	165-171	7	4
β-strand	174-175	2	4
α-helix	177-179	3
β-strand	181-183	3	4
α-helix	187-198	12
α-helix	202-203	2
α-helix	206-208	3
β-strand	209-211	3	5
β-strand	217-218	2	5
α-helix	227-234	8
α-helix	235-239	5
α-helix	240-245	6
α-helix	256-261	6
α-helix	266-268	3
β-strand	269-271	3	6
β-strand	277-279	3	6
α-helix	282-290	9
α-helix	297-299	3
α-helix	385-394	10
α-helix	401-406	6
β-strand	408-411	4	4
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	4
α-helix	445-449	5
α-helix	451-460	10
α-helix	469	1
β-strand	470-471	2	1
α-helix	472-477	6

Chain B: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	7
β-strand	25-30	6	7
β-strand	38-41	4	7
β-strand	43-47	5	8
α-helix	54-55	2
β-strand	56	1	8
α-helix	59-62	4
β-strand	69-73	5	8
β-strand	75-76	2	9
β-strand	79-80	2	9
α-helix	83-96	14
β-strand	108-112	5	7
α-helix	118-125	8
α-helix	126-131	6
β-strand	137-141	5	7
α-helix	142-150	9
β-strand	155-160	6	10
β-strand	165-171	7	10
β-strand	174-175	2	10
α-helix	177-179	3
β-strand	181-183	3	10
α-helix	187-198	12
α-helix	202-203	2
β-strand	209-211	3	11
β-strand	217-218	2	11
α-helix	227-234	8
α-helix	235-239	5
α-helix	240-245	6
α-helix	256-261	6
α-helix	266-268	3
β-strand	269-271	3	12
β-strand	277-279	3	12
α-helix	282-290	9
α-helix	297-299	3
β-strand	311	1	10
α-helix	385-394	10
α-helix	401-406	6
β-strand	408-411	4	10
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	10
α-helix	446-449	4
α-helix	451-460	10
α-helix	470-471	2
α-helix	474-477	4

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	13
β-strand	16-21	6	13
β-strand	29-32	4	13
β-strand	35-38	4	14
β-strand	53-54	2	14
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	14
β-strand	71	1	15
β-strand	76	1	15
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	13
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	13
α-helix	137-144	8
β-strand	150-155	6	16
β-strand	160-166	7	16
β-strand	169-170	2	16
β-strand	176-178	3	16
α-helix	182-195	14
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	17
β-strand	247-250	4	17
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-295	9
β-strand	297-300	4	16
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	16
α-helix	335-337	3
α-helix	338-346	9
α-helix	351-354	4
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain D: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	18
β-strand	16-21	6	18
β-strand	29-32	4	18
β-strand	35-38	4	19
β-strand	53-54	2	19
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	19
β-strand	71	1	20
β-strand	76	1	20
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	18
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	18
α-helix	137-144	8
β-strand	150-155	6	21
β-strand	160-166	7	21
β-strand	169-170	2	21
β-strand	176-178	3	21
α-helix	182-195	14
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	22
β-strand	247-250	4	22
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-295	9
β-strand	297-300	4	21
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	21
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-355	4
β-strand	357-358	2	18
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain E: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	268-272	5	23
β-strand	277-281	5	23
β-strand	289-292	4	23
β-strand	295-298	4	24
α-helix	321-341	21
α-helix	351-353	3
β-strand	357-360	4	25
β-strand	377	1	26
β-strand	384-385	2	24
α-helix	387-390	4
β-strand	392	1	26
β-strand	397-400	4	24
β-strand	403-404	2	27
β-strand	407-408	2	27
α-helix	418-433	16
β-strand	434	1	28
β-strand	439	1	28
α-helix	442-447	6
β-strand	449-454	6	23
α-helix	460-468	9
α-helix	469-473	5
β-strand	478-483	6	23
α-helix	484-491	8
β-strand	498-503	6	29
β-strand	508-514	7	29
β-strand	517-518	2	29
α-helix	520-522	3
β-strand	524-526	3	29
α-helix	530-543	14
α-helix	558-569	12
β-strand	580-586	7	25
β-strand	593-600	8	25
α-helix	606-609	4
α-helix	610-612	3
α-helix	615-620	6
α-helix	622-624	3
α-helix	628-631	4
α-helix	635-637	3
β-strand	638	1	30
β-strand	645	1	30
α-helix	651-658	8
α-helix	668-676	9
α-helix	678-686	9
α-helix	703-716	14
α-helix	720-722	3
α-helix	723-728	6
β-strand	730-733	4	29
α-helix	735-738	4
α-helix	742-753	12
α-helix	756-758	3
α-helix	763-779	17
α-helix	793-815	23
β-strand	829	1	29
α-helix	841-850	10
α-helix	855-858	4
β-strand	860-861	2	23
α-helix	862-868	7
α-helix	869-874	6

Chain F: 34 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	265-267	3
β-strand	268-272	5	31
β-strand	277-281	5	31
β-strand	289-292	4	31
β-strand	295-298	4	32
α-helix	321-341	21
α-helix	351-353	3
β-strand	357-360	4	33
β-strand	377	1	34
β-strand	384-385	2	32
α-helix	387-390	4
β-strand	392	1	34
β-strand	397-400	4	32
β-strand	403-404	2	35
β-strand	407-408	2	35
α-helix	418-433	16
β-strand	434	1	36
β-strand	439	1	36
α-helix	442-447	6
β-strand	449-454	6	31
α-helix	460-468	9
α-helix	469-473	5
β-strand	478-483	6	31
α-helix	484-491	8
β-strand	498-503	6	37
β-strand	508-514	7	37
β-strand	517-518	2	37
α-helix	520-522	3
β-strand	524-526	3	37
α-helix	530-543	14
α-helix	556-569	14
β-strand	580-586	7	33
β-strand	593-600	8	33
α-helix	606-609	4
α-helix	610-612	3
α-helix	615-620	6
α-helix	622-624	3
α-helix	628-631	4
α-helix	635-637	3
β-strand	638	1	38
β-strand	645	1	38
α-helix	651-658	8
α-helix	668-676	9
α-helix	678-686	9
α-helix	703-716	14
α-helix	720-722	3
α-helix	723-728	6
β-strand	730-733	4	37
α-helix	736-738	3
α-helix	742-753	12
α-helix	756-758	3
α-helix	763-779	17
α-helix	785-787	3
α-helix	790-815	26
β-strand	829	1	37
α-helix	841-850	10
α-helix	855-858	4
β-strand	860-861	2	31
α-helix	862-868	7
α-helix	869-874	6

Chains G and H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	473-518	46
α-helix	522-556	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 4	A, B	protein	489	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P80428 (AlphaFold model)
Actin	C, D	protein	375	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P60010 (AlphaFold model)
Actin-like protein ARP8	E, F	protein	628	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12386 (AlphaFold model)
Putative DNA helicase INO80	G, H	protein	147	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53115 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5NBN_1 Actin-related protein 4 (chains A, B)
MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQ
SIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTEN
RKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKST
RRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQ
ECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDI
PANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSAD
TPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGL
SDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGV
ERLLNDRFR

Sequence of entity 2 (C, D), FASTA

>5NBN_2 Actin (chains C, D)
MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQS
KRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMT
QIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDL
AGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSY
ELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMS
GGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQ
EYDESGPSIVHHKCF

Sequence of entity 3 (E, F), FASTA

>5NBN_3 Actin-like protein ARP8 (chains E, F)
MPLNDEIDLNDPTATIVIHPGSNSIKIGFPKDDHPVVVPNCVAVPKKWLDLENSEHVENV
CLQREQSEEFNNIKSEMEKNFRERMRYYKRKVPGNAHEQVVSFNENSKPEIISEKNDPSP
IEWIFDDSKLYYGSDALRCVDEKFVIRKPFRGGSFNVKSPYYKSLAELISDVTKLLEHAL
NSETLNVKPTKFNQYKVVLVIPDIFKKSHVETFIRVLLTELQFQAVAIIQESLATCYGAG
ISTSTCVVNIGAAETRIACVDEGTVLEHSAITLDYGGDDITRLFALFLLQSDFPLQDWKI
DSKHGWLLAERLKKNFTTFQDADVAVQLYNFMNRSPNQPTEKYEFKLFDEVMLAPLALFF
PQIFKLIRTSSHKNSSLEFQLPESRDLFTNELNDWNSLSQFESKEGNLYCDLNDDLKILN
RILDAHNIIDQLQDKPENYGNTLKENFAPLEKAIVQSIANASITADVTRMNSFYSNILIV
GGSSKIPALDFILTDRINIWRPSLLSSASFPQFYKKLTKEIKDLEGHYVNAPDKTEDENK
QILQAQIKEKIVEELEEQHQNIEHQNGNEHIFPVSIIPPPRDMNPALIIWKGASVLAQIK
LVEELFITNSDWDVHGSRILQYKCIFTY

Sequence of entity 4 (G, H), FASTA

>5NBN_4 Putative DNA helicase INO80 (chains G, H)
MARAIQRHYDNTYTTIWKDMARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSK
NFKQIKDFQTRARRGIREMSNFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKK
LNFLLTQTELYSHFIGRKNWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
LAR	Latrunculin a	C22 H31 N O5 S	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
CA	Calcium ion	Ca	4

Primary citation

The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Knoll, K.R., Eustermann, S., Niebauer, V. et al. Nat Struct Mol Biol (2018) 25:823-832. DOI 10.1038/s41594-018-0115-8 · PubMed

Other PDB entries of the same protein (UniProt P80428 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5I9E 2.8 Å, Crystal structure of a nuclear actin ternary complex
5NBL 2.8 Å, Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody
7VVY 3.1 Å, TRA module of NuA4
8ESC 3.1 Å, Structure of the Yeast NuA4 Histone Acetyltransferase Complex
8A5O 3.2 Å, Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80
8A5A 3.3 Å, Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80
5NBM 3.4 Å, Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody
3QB0 3.4 Å, Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP
7YFN 3.8 Å, Core module of the NuA4 complex in S. cerevisiae
7YFP 4.0 Å, The NuA4 histone acetyltransferase complex from S. cerevisiae
5Y81 4.7 Å, NuA4 TEEAA sub-complex
7VVZ 8.8 Å, NuA4 bound to the nucleosome

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