5I9E: Nuclear actin ternary complex

Crystal structure of a nuclear actin ternary complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 27 Jul 2016.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces bayanus
Chains: 6
Atoms: 12,666
Mol. weight: 213.02 kDa
Ligands: ATP, MG
Released: 27 Jul 2016

Explore 5I9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I9E contains 95 α-helices and 82 β-strands across 6 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	17-21	5	2
β-strand	25-30	6	2
β-strand	38-41	4	2
β-strand	43-47	5	3
β-strand	55-56	2	3
α-helix	59-62	4
β-strand	69-73	5	3
β-strand	75-76	2	4
β-strand	79-80	2	4
α-helix	83-96	14
β-strand	107-112	6	2
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	2
α-helix	142-149	8
β-strand	155-160	6	5
β-strand	165-171	7	5
β-strand	174-175	2	5
β-strand	181-183	3	5
α-helix	187-197	11
β-strand	209-211	3	6
β-strand	217-218	2	6
α-helix	219-220	2
α-helix	227-233	7
α-helix	234-238	5
α-helix	239-245	7
α-helix	254-256	3
α-helix	258-261	4
α-helix	266-268	3
β-strand	270-271	2	7
β-strand	277-278	2	7
α-helix	282-290	9
α-helix	385-395	11
α-helix	398-406	9
β-strand	408-411	4	5
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	5
α-helix	446-448	3
α-helix	451-459	9
β-strand	462	1	1
α-helix	463-468	6
α-helix	469	1
β-strand	470-471	2	2
α-helix	472-478	7

Chain B: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	8
β-strand	16-21	6	8
β-strand	22	1	9
β-strand	24	1	9
β-strand	29-32	4	8
β-strand	35-36	2	10
β-strand	53-54	2	10
α-helix	56-60	5
α-helix	66	1
β-strand	67-68	2	10
β-strand	71-72	2	11
β-strand	75-76	2	11
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	8
α-helix	113-121	9
α-helix	122-126	5
β-strand	132-136	5	8
α-helix	137-144	8
β-strand	150-155	6	12
β-strand	160-166	7	12
β-strand	169-170	2	12
β-strand	176-178	3	12
α-helix	182-194	13
α-helix	206-215	10
α-helix	223-231	9
β-strand	238-241	4	13
β-strand	247-250	4	13
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	12
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	12
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
α-helix	359-365	7
α-helix	366-369	4
α-helix	370-373	4

Chain C: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	14
β-strand	25-30	6	14
β-strand	38-41	4	14
β-strand	43-47	5	15
β-strand	55-56	2	15
α-helix	59-62	4
β-strand	69-73	5	15
β-strand	75-76	2	16
β-strand	79-80	2	16
α-helix	83-96	14
β-strand	107-112	6	14
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	14
α-helix	142-149	8
β-strand	155-160	6	17
β-strand	165-171	7	17
β-strand	174-175	2	17
α-helix	177-179	3
β-strand	181-183	3	17
α-helix	187-197	11
β-strand	209-211	3	18
β-strand	217-218	2	18
α-helix	227-233	7
α-helix	234-238	5
α-helix	239-245	7
α-helix	258-261	4
α-helix	266-268	3
β-strand	270-271	2	19
β-strand	277-278	2	19
α-helix	282-290	9
α-helix	301	1
α-helix	385-395	11
α-helix	398-406	9
β-strand	408-411	4	17
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	17
α-helix	445-448	4
α-helix	451-459	9
α-helix	464-468	5
β-strand	470-471	2	14
α-helix	472-478	7

Chain D: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	20
β-strand	16-21	6	20
β-strand	22	1	21
β-strand	24	1	21
β-strand	29-32	4	20
β-strand	35-36	2	22
β-strand	53-54	2	22
α-helix	56-60	5
α-helix	65-66	2
β-strand	67-68	2	22
β-strand	71-72	2	23
β-strand	75-76	2	23
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	20
α-helix	113-121	9
α-helix	122-126	5
β-strand	132-136	5	20
α-helix	137-144	8
β-strand	150-155	6	24
β-strand	160-166	7	24
β-strand	169-170	2	24
β-strand	176-178	3	24
α-helix	182-194	13
α-helix	206-216	11
α-helix	223-231	9
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-294	8
β-strand	297-300	4	24
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	24
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-355	4
α-helix	359-365	7
α-helix	366-369	4
α-helix	370-373	4

Chains E and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	353-389	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 4	A, C	protein	490	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P80428 (AlphaFold model)
Actin	B, D	protein	375	Saccharomyces bayanus	P60011 (AlphaFold model)
Helicase SWR1	E, H	protein	77	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q05471 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5I9E_1 Actin-related protein 4 (chains A, C)
PMSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSE
QSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTE
NRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKS
TRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFF
QECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDD
IPANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSA
DTPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPG
LSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVG
VERLLNDRFR

Sequence of entity 2 (B, D), FASTA

>5I9E_2 Actin (chains B, D)
MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQS
KRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMT
QIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDL
AGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSY
ELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMS
GGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQ
EYDESGPSIVHHKCF

Sequence of entity 3 (E, H), FASTA

>5I9E_3 Helicase SWR1 (chains E, H)
SYFYKQQDLQIHTDHLINQGIHMSKLFRSSTKARIARAKKVSQMIEQHFKHVAGAEERKA
KEEERHKKSLAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	4

Primary citation

Crystal structure of a nuclear actin ternary complex. Cao, T., Sun, L., Jiang, Y. et al. Proc Natl Acad Sci U S A (2016) 113:8985-8990. DOI 10.1073/pnas.1602818113 · PubMed

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

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
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

Browse structure collections

About this viewer

MolViewer shows 5I9E 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.