3UKU: Arp2/3 complex with bound inhibitor CK-869

Structure of Arp2/3 complex with bound inhibitor CK-869. Determined by X-ray diffraction at 2.75 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Bos taurus
Chains: 7
Atoms: 13,460
Mol. weight: 224.59 kDa
Ligands: C69
Released: 13 Feb 2013

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

Secondary structure: helices and β-sheets

3UKU contains 82 α-helices and 90 β-strands across 7 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, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-10	3	1
β-strand	11-12	2	2
β-strand	16-19	4	2
β-strand	21	1	1
β-strand	22	1	3
β-strand	24	1	3
β-strand	29-32	4	2
β-strand	35-37	3	4
β-strand	61-62	2	4
α-helix	63-66	4
β-strand	73-75	3	4
α-helix	86-95	10
α-helix	96-100	5
α-helix	105-107	3
β-strand	109-114	6	1
α-helix	120-127	8
α-helix	128-133	6
β-strand	138-143	6	1
α-helix	144-151	8
β-strand	165-170	6	5
β-strand	175-181	7	5
β-strand	184-185	2	5
α-helix	187-189	3
β-strand	191-193	3	5
α-helix	197-209	13
α-helix	220-231	12
α-helix	238-247	10
α-helix	249-252	4
β-strand	254-259	6	6
β-strand	266-271	6	6
α-helix	274-277	4
α-helix	279-282	4
α-helix	285-287	3
α-helix	296-305	10
α-helix	309-311	3
α-helix	313-316	4
β-strand	319-322	4	5
α-helix	324-326	3
α-helix	331-349	19
β-strand	367-368	2	5
α-helix	373-375	3
α-helix	376-384	9
α-helix	388-392	5
β-strand	395-396	2	1
α-helix	397-403	7
α-helix	405-409	5

Chain B: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	155-159	5	7
β-strand	164-168	5	7
β-strand	169	1	8
β-strand	174	1	8
β-strand	180-182	3	7
α-helix	187-198	12
α-helix	210-220	11
α-helix	227-236	10
β-strand	242-245	4	9
β-strand	251-254	4	9
α-helix	256-258	3
α-helix	262-266	5
α-helix	268-271	4
α-helix	277-287	11
α-helix	291-293	3
α-helix	294-299	6
β-strand	301-304	4	7
α-helix	306-308	3
α-helix	313-328	16
α-helix	337-339	3
β-strand	344-345	2	7

Chain C: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
α-helix	10-11	2
β-strand	14-16	3	11
β-strand	22-25	4	11
β-strand	31-38	8	11
β-strand	41-49	9	11
β-strand	57-61	5	12
β-strand	66-70	5	12
β-strand	76-82	7	12
β-strand	85-90	6	12
β-strand	99-104	6	13
β-strand	110-115	6	13
β-strand	120-126	7	13
β-strand	131-137	7	13
β-strand	145-150	6	14
β-strand	156-161	6	14
β-strand	166-170	5	14
α-helix	180-182	3
β-strand	183	1	15
β-strand	186	1	15
β-strand	196-197	2	14
β-strand	205-210	6	16
β-strand	216-221	6	16
β-strand	225-230	6	16
α-helix	231-233	3
β-strand	236-241	6	16
α-helix	245-246	2
β-strand	247	1	17
β-strand	251-252	2	18
β-strand	257-260	4	18
β-strand	262	1	17
β-strand	268-273	6	18
β-strand	278-284	7	18
β-strand	329-336	8	10
β-strand	344-349	6	10
β-strand	353-358	6	10
α-helix	359-365	7

Chain D: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-23	15
β-strand	32-37	6	19
β-strand	41-46	6	19
α-helix	48-50	3
β-strand	54-60	7	19
α-helix	64-68	5
α-helix	72-80	9
α-helix	81-83	3
β-strand	84-85	2	19
α-helix	87-88	2
β-strand	89	1	20
β-strand	91	1	20
β-strand	93-98	6	19
α-helix	107-114	8
α-helix	116-132	17
β-strand	142-147	6	21
β-strand	150-155	6	21
β-strand	161-166	6	21
β-strand	167-168	2	22
α-helix	174-185	12
α-helix	188-190	3
β-strand	197-199	3	21
β-strand	202	1	22
β-strand	220-221	2	22
β-strand	224-227	4	21
α-helix	229-232	4
α-helix	238-244	7
α-helix	247-277	31

Chain E: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	15-16	2	23
β-strand	19-20	2	23
β-strand	24	1	24
β-strand	34	1	24
α-helix	41-52	12
α-helix	63-82	20
α-helix	88-100	13
α-helix	118-120	3
α-helix	123-143	21
α-helix	145-148	4
β-strand	149	1	25
β-strand	156	1	25
α-helix	158-161	4
α-helix	162-165	4
α-helix	168-170	3

Chain F: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	26	1	26
β-strand	34	1	26
α-helix	37-40	4
α-helix	44-46	3
β-strand	47-54	8	27
β-strand	60-66	7	27
β-strand	69-75	7	27
α-helix	81-96	16
β-strand	104	1	27
β-strand	114-119	6	27
α-helix	120-125	6
α-helix	128-165	38

Chain G: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	11-13	3
α-helix	39-46	8
α-helix	51-58	8
α-helix	69-84	16
α-helix	88-90	3
α-helix	91-95	5
α-helix	100-113	14
α-helix	125-136	12
α-helix	139-146	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-like protein 3	A	protein	418	Bos taurus	P61157 (AlphaFold model)
Actin-like protein 2	B	protein	394	Bos taurus	A7MB62 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1B	C	protein	372	Bos taurus	Q58CQ2 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D	protein	300	Bos taurus	Q3MHR7 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E	protein	178	Bos taurus	Q3T035
Actin-related protein 2/3 complex subunit 4	F	protein	168	Bos taurus	Q148J6
Actin-related protein 2/3 complex subunit 5	G	protein	151	Bos taurus	Q3SYX9

Sequence of entity 1 (A), FASTA

>3UKU_1 ACTIN-LIKE PROTEIN 3 (chains A)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Sequence of entity 2 (B), FASTA

>3UKU_2 ACTIN-LIKE PROTEIN 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Sequence of entity 3 (C), FASTA

>3UKU_3 Actin-related protein 2/3 complex subunit 1B (chains C)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDW
APDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVR
SLESALKDLKIV

Sequence of entity 4 (D), FASTA

>3UKU_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 5 (E), FASTA

>3UKU_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Sequence of entity 6 (F), FASTA

>3UKU_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>3UKU_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MSKNTVSSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Ligands and cofactors

ID	Name	Formula	Copies
C69	(2S)-2-(3-bromophenyl)-3-(2,4-dimethoxyphenyl)-1,3-thiazolidin-4-one	C17 H16 Br N O3 S	1

Primary citation

Structure of Arp2/3 complex with bound inhibitor CK-869. Nolen, B.J., Han, M. To be published.

Other PDB entries of the same protein (UniProt P61157 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K8K 2.0 Å, Crystal Structure of Arp2/3 Complex
2P9I 2.46 Å, Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with…
3UKR 2.48 Å, Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666
3ULE 2.5 Å, Structure of Bos taurus Arp2/3 complex with bound inhibitor CK-869 and ATP
1TYQ 2.55 Å, Crystal structure of Arp2/3 complex with bound ATP and calcium
1U2V 2.55 Å, Crystal structure of Arp2/3 complex with bound ADP and calcium
2P9K 2.59 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with…
2P9L 2.65 Å, Crystal Structure of bovine Arp2/3 complex
3RSE 2.65 Å, Structural and biochemical characterization of two binding sites for nucleation…
2P9S 2.68 Å, Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+
3DXK 2.7 Å, Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636
2P9U 2.75 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium

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