3QB0: Actin-related protein Arp4 from S. cerevisiae

Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP. Determined by X-ray diffraction at 3.4 Å resolution. Released 4 May 2011.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 13,785
Mol. weight: 226.64 kDa
Ligands: CA, ATP
Released: 4 May 2011

Explore 3QB0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QB0 contains 102 α-helices and 92 β-strands across 4 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: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
β-strand	17-20	4	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	61-63	3
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	108-112	5	2
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	2
α-helix	142-150	9
β-strand	155-160	6	5
β-strand	165-171	7	5
β-strand	174-175	2	5
α-helix	177-179	3
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	227-234	8
α-helix	235-239	5
α-helix	240-245	6
α-helix	254-263	10
β-strand	268-271	4	7
β-strand	277-280	4	7
α-helix	282-290	9
α-helix	297-299	3
α-helix	321-323	3
β-strand	324	1	8
α-helix	325	1
α-helix	385-394	10
α-helix	401-405	5
β-strand	408-411	4	5
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	5
α-helix	446-449	4
α-helix	451-460	10
α-helix	463-467	5
β-strand	470-471	2	2
α-helix	472-476	5
α-helix	481-483	3
α-helix	484-488	5

Chain B: 25 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	9
β-strand	17-20	4	10
β-strand	25-30	6	10
β-strand	38-41	4	10
β-strand	43-47	5	11
β-strand	55-56	2	11
β-strand	69-73	5	11
β-strand	75-76	2	12
β-strand	79-80	2	12
α-helix	83-96	14
β-strand	107-112	6	10
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	10
α-helix	142-150	9
β-strand	155-160	6	13
β-strand	165-171	7	13
β-strand	174-175	2	13
α-helix	177-179	3
β-strand	181-183	3	13
α-helix	187-197	11
β-strand	209-211	3	14
β-strand	217-218	2	14
α-helix	219-220	2
α-helix	227-234	8
α-helix	235-239	5
α-helix	240-245	6
α-helix	254-263	10
β-strand	268-271	4	15
β-strand	277-280	4	15
α-helix	282-290	9
α-helix	301	1
α-helix	321-323	3
β-strand	324	1	16
α-helix	325	1
α-helix	385-394	10
α-helix	401-405	5
β-strand	408-411	4	13
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	13
α-helix	445-449	5
α-helix	451-460	10
α-helix	464-467	4
β-strand	470-471	2	10
α-helix	472-476	5
α-helix	481-483	3
α-helix	484-488	5

Chain C: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	8
β-strand	17-20	4	17
β-strand	25-30	6	17
β-strand	38-41	4	17
β-strand	43-47	5	18
β-strand	55-56	2	18
α-helix	61-63	3
β-strand	69-73	5	18
β-strand	75-76	2	19
β-strand	79-80	2	19
α-helix	83-96	14
β-strand	107-112	6	17
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	17
α-helix	142-150	9
β-strand	155-160	6	20
β-strand	165-171	7	20
β-strand	174-175	2	20
α-helix	177-179	3
β-strand	181-183	3	20
α-helix	187-197	11
β-strand	209-211	3	21
β-strand	217-218	2	21
α-helix	219-220	2
α-helix	227-234	8
α-helix	235-239	5
α-helix	240-245	6
α-helix	254-263	10
β-strand	268-271	4	22
β-strand	277-280	4	22
α-helix	282-290	9
α-helix	301	1
α-helix	321-323	3
β-strand	324	1	1
α-helix	325	1
α-helix	385-394	10
α-helix	401-405	5
β-strand	408-411	4	20
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	20
α-helix	445-449	5
α-helix	451-460	10
α-helix	464-467	4
β-strand	470-471	2	17
α-helix	472-476	5
α-helix	481-483	3
α-helix	484-488	5

Chain D: 25 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	16
β-strand	17-20	4	23
β-strand	25-30	6	23
β-strand	38-41	4	23
β-strand	43-47	5	24
β-strand	55-56	2	24
α-helix	61-63	3
β-strand	69-73	5	24
β-strand	75-76	2	25
β-strand	79-80	2	25
α-helix	83-96	14
β-strand	107-112	6	23
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-141	6	23
α-helix	142-150	9
β-strand	155-160	6	26
β-strand	165-171	7	26
β-strand	174-175	2	26
α-helix	177-179	3
β-strand	181-183	3	26
α-helix	187-197	11
β-strand	209-211	3	27
β-strand	217-218	2	27
α-helix	219-220	2
α-helix	227-234	8
α-helix	235-239	5
α-helix	240-245	6
α-helix	254-263	10
β-strand	268-271	4	28
β-strand	277-280	4	28
α-helix	282-290	9
α-helix	321-323	3
β-strand	324	1	9
α-helix	325	1
α-helix	385-394	10
α-helix	401-405	5
β-strand	408-411	4	26
α-helix	413-416	4
α-helix	420-431	12
β-strand	439-440	2	26
α-helix	446-449	4
α-helix	451-460	10
α-helix	463-467	5
β-strand	470-471	2	23
α-helix	472-476	5
α-helix	481-483	3
α-helix	484-488	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 4	A, B, C, D	protein	498	Saccharomyces cerevisiae	P80428 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3QB0_1 Actin-related protein 4 (chains A, B, C, D)
MKHHHHHHKMSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADE
GNKKIFSEQSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLT
EPVWNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIV
DGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYD
YANNRGFFQECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEE
LFLPKEDDIPANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKS
TSPAANSADTPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLT
GGTSSIPGLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVG
KKEYEEVGVERLLNDRFR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4

Primary citation

Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin. Fenn, S., Breitsprecher, D., Gerhold, C.B. et al. EMBO J (2011) 30:2153-2166. DOI 10.1038/emboj.2011.118 · 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
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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