5NBM: Actin-related protein 4

Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody. Determined by X-ray diffraction at 3.4 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos, Trichoplusia ni
Chains: 8
Atoms: 14,077
Mol. weight: 232.72 kDa
Ligands: CA, ATP
Released: 22 Aug 2018

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

Secondary structure: helices and β-sheets

5NBM contains 105 α-helices and 105 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: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	1
β-strand	25-30	6	1
β-strand	38-41	4	1
β-strand	43-47	5	2
α-helix	53-55	3
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	107-112	6	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	206-208	3
β-strand	209-211	3	5
β-strand	217-218	2	5
α-helix	219-220	2
α-helix	227-236	10
α-helix	238-245	8
α-helix	256-261	6
β-strand	262	1	6
β-strand	265	1	6
α-helix	266-267	2
β-strand	268-271	4	7
β-strand	277-280	4	7
α-helix	282-290	9
α-helix	297-299	3
β-strand	311	1	4
α-helix	385-394	10
α-helix	400-405	6
β-strand	408-411	4	4
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-441	3	4
α-helix	445-449	5
α-helix	451-461	11
β-strand	470-471	2	1
α-helix	472-478	7

Chain B: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	8
β-strand	25-30	6	8
β-strand	38-41	4	8
β-strand	43-47	5	9
α-helix	54-55	2
β-strand	56	1	9
α-helix	59-62	4
β-strand	69-73	5	9
β-strand	75-76	2	10
β-strand	79-80	2	10
α-helix	83-96	14
β-strand	107-112	6	8
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	8
α-helix	142-150	9
β-strand	155-160	6	11
β-strand	165-171	7	11
β-strand	174-175	2	11
α-helix	177-179	3
β-strand	181-183	3	11
α-helix	187-198	12
α-helix	206-208	3
β-strand	209-211	3	12
β-strand	217-218	2	12
α-helix	219-220	2
α-helix	227-236	10
α-helix	238-245	8
α-helix	256-261	6
α-helix	266-267	2
β-strand	269-271	3	13
β-strand	277-279	3	13
α-helix	282-290	9
α-helix	297-299	3
β-strand	311	1	11
α-helix	385-394	10
α-helix	398-405	8
β-strand	408-411	4	11
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	11
α-helix	445-449	5
α-helix	451-461	11
α-helix	466-468	3
β-strand	470-471	2	8
α-helix	472-478	7

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	14
β-strand	16-21	6	14
β-strand	29-32	4	14
β-strand	35-38	4	15
β-strand	53-54	2	15
α-helix	56-59	4
α-helix	62-64	3
β-strand	65-68	4	15
β-strand	71	1	16
β-strand	76	1	16
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	14
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	14
α-helix	137-144	8
β-strand	150-155	6	17
β-strand	160-166	7	17
β-strand	169-170	2	17
α-helix	172-174	3
β-strand	176-178	3	17
α-helix	182-195	14
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	18
β-strand	247-250	4	18
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-284	11
α-helix	287-289	3
α-helix	290-295	6
β-strand	297-300	4	17
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	17
α-helix	335-337	3
α-helix	338-346	9
α-helix	351-354	4
β-strand	357-358	2	14
α-helix	359-365	7
α-helix	369-373	5

Chain D: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	19
β-strand	16-21	6	19
β-strand	29-32	4	19
β-strand	35-38	4	20
β-strand	53-54	2	20
α-helix	56-59	4
β-strand	65-68	4	20
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	19
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	19
α-helix	137-144	8
β-strand	150-155	6	21
β-strand	160-166	7	21
β-strand	169-170	2	21
α-helix	172-174	3
β-strand	176-178	3	21
α-helix	182-195	14
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	22
β-strand	247-250	4	22
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-284	11
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	350-354	5
β-strand	357-358	2	19
α-helix	359-365	7
α-helix	367-371	5

Chain E: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	23
β-strand	13-15	3	24
β-strand	20-28	9	23
α-helix	31-33	3
β-strand	35-41	7	25
α-helix	46-47	2
β-strand	48-53	6	25
β-strand	60-62	3	25
β-strand	71-75	5	23
α-helix	76-78	3
β-strand	80-85	6	23
α-helix	90-92	3
β-strand	94-101	8	25
β-strand	115-116	2	25
β-strand	120-122	3	25
β-strand	123-125	3	24

Chain F: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	26
β-strand	12-15	4	27
β-strand	20-28	9	26
α-helix	31-33	3
β-strand	35-41	7	27
α-helix	46-47	2
β-strand	48-53	6	27
β-strand	60-62	3	27
β-strand	71-75	5	26
α-helix	76-78	3
β-strand	80-85	6	26
α-helix	90-92	3
β-strand	94-101	8	27
β-strand	115-116	2	27
β-strand	120-125	6	27

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13

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)
nAct-Nanobody	E, F	protein	159	Vicugna pacos
Unknown peptide	G, H	protein	17	Trichoplusia ni

Sequence of entity 1 (A, B), FASTA

>5NBM_1 Actin-related protein 4 (chains A, B)
MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQ
SIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTEN
RKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKST
RRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQ
ECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDI
PANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSAD
TPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGL
SDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGV
ERLLNDRFR

Sequence of entity 2 (C, D), FASTA

>5NBM_2 Actin (chains C, D)
MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQS
KRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMT
QIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDL
AGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSY
ELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMS
GGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQ
EYDESGPSIVHHKCF

Sequence of entity 3 (E, F), FASTA

>5NBM_3 nAct-Nanobody (chains E, F)
MAQVQLVESGGGSVQAGDSLRLSCTASGRTFTNYGMGWFRQAPGKEREFVAAIGRFGFPL
YYSDSVKGRFTISRDNAKTTVYLQMHNLKPEDTAIYFCAARNPRATAEDVSAYDYWGQGT
QVTVSSKGSSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 4 (G, H), FASTA

>5NBM_4 Unknown peptide (chains G, H)
XXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	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
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
5NBN 4.0 Å, Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80
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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