6UHC: Human Arp2/3 complex with bound NPFs

CryoEM structure of human Arp2/3 complex with bound NPFs. Determined by electron microscopy at 3.9 Å resolution. Released 1 Jul 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 9
Atoms: 14,680
Mol. weight: 336.62 kDa
Ligands: MG, ATP
Released: 1 Jul 2020

Explore 6UHC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UHC contains 93 α-helices and 92 β-strands across 9 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: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-37	3	2
α-helix	56-58	3
β-strand	61-62	2	2
α-helix	63-66	4
β-strand	73-75	3	2
β-strand	78-79	2	3
β-strand	82-83	2	3
α-helix	86-95	10
α-helix	96-101	6
α-helix	105-107	3
β-strand	110-114	5	1
α-helix	120-123	4
α-helix	125-131	7
β-strand	138-143	6	1
α-helix	144-151	8
α-helix	152-154	3
β-strand	165-170	6	4
β-strand	175-180	6	4
β-strand	185	1	4
β-strand	191-193	3	4
α-helix	197-211	15
α-helix	217-219	3
α-helix	220-231	12
α-helix	238-247	10
β-strand	254-259	6	5
β-strand	266-271	6	5
α-helix	277-280	4
α-helix	285-287	3
α-helix	296-306	11
α-helix	309-311	3
α-helix	312-316	5
β-strand	319-322	4	4
α-helix	324-326	3
α-helix	331-352	22
β-strand	367	1	4
α-helix	376-386	11
α-helix	389-393	5
β-strand	395-396	2	1
α-helix	397-402	6
α-helix	405-409	5

Chain B: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	6
β-strand	17-21	5	6
β-strand	30-33	4	6
β-strand	36-39	4	7
β-strand	56-57	2	7
α-helix	59-63	5
α-helix	65-67	3
β-strand	68-71	4	7
β-strand	74-75	2	8
β-strand	78-79	2	8
α-helix	82-93	12
α-helix	102-104	3
β-strand	106-111	6	6
α-helix	112	1
α-helix	117-126	10
α-helix	127-131	5
β-strand	135-140	6	6
α-helix	144-147	4
β-strand	154	1	9
β-strand	155-159	5	10
β-strand	164-166	3	10
β-strand	169	1	9
α-helix	173-175	3
α-helix	176-178	3
β-strand	180-182	3	10
α-helix	186-199	14
α-helix	210-220	11
α-helix	227-236	10
β-strand	242-245	4	11
β-strand	251-254	4	11
α-helix	257-260	4
α-helix	262-265	4
α-helix	278-287	10
α-helix	291-298	8
β-strand	301-304	4	10
α-helix	306-308	3
α-helix	313-328	16
α-helix	335-338	4
β-strand	344-345	2	10
α-helix	354-364	11
β-strand	373-374	2	6
α-helix	375-379	5

Chain C: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	14-16	3	13
β-strand	22-25	4	13
β-strand	31-38	8	13
β-strand	41-49	9	13
β-strand	55-61	7	14
β-strand	66-71	6	14
β-strand	76-82	7	14
β-strand	85-91	7	14
β-strand	102-104	3	15
β-strand	110-114	5	15
β-strand	120-126	7	15
β-strand	131-137	7	15
β-strand	145-150	6	16
β-strand	156-161	6	16
β-strand	167-170	4	16
α-helix	178-182	5
β-strand	183	1	17
β-strand	186	1	17
β-strand	194-197	4	16
β-strand	205-210	6	18
β-strand	216-221	6	18
β-strand	225-230	6	18
α-helix	231-233	3
β-strand	236-241	6	18
β-strand	247-254	8	19
β-strand	257-262	6	19
β-strand	268-273	6	19
β-strand	278-284	7	19
β-strand	329-336	8	12
β-strand	341	1	19
β-strand	344-349	6	12
β-strand	353-358	6	12
α-helix	359-365	7

Chain D: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-22	14
α-helix	26-30	5
β-strand	32-37	6	20
β-strand	41-46	6	20
α-helix	48-50	3
β-strand	54-60	7	20
α-helix	64-68	5
α-helix	72-80	9
β-strand	84-85	2	20
α-helix	87-88	2
β-strand	93-98	6	20
α-helix	107-114	8
α-helix	116-121	6
α-helix	123-134	12
α-helix	139-141	3
β-strand	142-147	6	21
β-strand	150-156	7	21
β-strand	161-168	8	21
α-helix	172-186	15
β-strand	197-201	5	21
α-helix	205-206	2
β-strand	220-227	8	21
α-helix	229-232	4
α-helix	234-236	3
α-helix	237-244	8
α-helix	247-280	34

Chain E: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	22
β-strand	19-20	2	22
α-helix	32-34	3
α-helix	41-52	12
α-helix	63-82	20
α-helix	88-100	13
β-strand	106	1	23
β-strand	108	1	23
α-helix	118-119	2
α-helix	124-148	25
β-strand	149	1	24
β-strand	156	1	24
α-helix	158-161	4
α-helix	168-170	3

Chain F: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
α-helix	37-40	4
α-helix	44-46	3
β-strand	47	1	25
α-helix	48-50	3
β-strand	51-54	4	25
β-strand	60-66	7	25
β-strand	69-75	7	25
α-helix	76-77	2
α-helix	81-96	16
β-strand	104	1	25
α-helix	108-109	2
β-strand	114-119	6	25
α-helix	120-125	6
α-helix	128-165	38

Chain G: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	39-48	10
α-helix	51-58	8
α-helix	69-85	17
α-helix	88-90	3
α-helix	91-95	5
α-helix	100-113	14
α-helix	121-146	26

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	463-466	4
α-helix	472-475	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 3	A	protein	418	Homo sapiens	P61158 (AlphaFold model)
Actin-related protein 2	B	protein	394	Homo sapiens	P61160 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1B	C	protein	372	Homo sapiens	O15143 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D	protein	300	Homo sapiens	O15144 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E	protein	203	Homo sapiens	O15145
Actin-related protein 2/3 complex subunit 4	F	protein	168	Homo sapiens	P59998
Actin-related protein 2/3 complex subunit 5	G	protein	151	Homo sapiens	O15511
Neural Wiskott-Aldrich syndrome protein	H, I	protein	501	Mus musculus	Q91YD9

Sequence of entity 1 (A), FASTA

>6UHC_1 Actin-related protein 3 (chains A)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Sequence of entity 2 (B), FASTA

>6UHC_2 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Sequence of entity 3 (C), FASTA

>6UHC_3 Actin-related protein 2/3 complex subunit 1B (chains C)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWTKVHELKEHNGQVTGIDW
APESNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSASGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLALTFITDNSLVAAGHDCFPVLFTYDAAAGMLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGGTAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVK
SLESALKDLKIK

Sequence of entity 4 (D), FASTA

>6UHC_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSFLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 5 (E), FASTA

>6UHC_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQGT
SENLYQGGGDYKDDDDKCGRASS

Sequence of entity 6 (F), FASTA

>6UHC_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>6UHC_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAMLLQWHEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H, I), FASTA

>6UHC_8 Neural Wiskott-Aldrich syndrome protein (chains H, I)
MSSGQQPPRRVTNVGSLLLTPQENESLFSFLGKKCVTMSSAVVQLYAADRNCMWAKKCSG
VACLVKDNPQRSYFLRIFDIKDGKLLWEQELYNNFVYNSPRGYFHTFAGDTCQVALNFAN
EEEAKKFRKAVTDLLGRRQRKSEKRRDAPNGPNLPMATVDIKNPEITTNRFYGSQVNNIS
HTKEKKKGKAKKKRLTKADIGTPSNFQHIGHVGWDPNTGFDLNNLDPELKNLFDMCGISE
AQLKDRETSKVIYDFIEKTGGVEAVKNELRRQAPPPPPPSRGGPPPPPPPPHSSGPPPPP
ARGRGAPPPPPSRAPTAAPPPPPPSRPGVVVPPPPPNRMYPPPPPALPSSAPSGPPPPPP
PSMAGSTAPPPPPPPPPPPGPPPPPGLPSDGDHQVPAPSGNKAALLDQIREGAQLKKVEQ
NSRPVSCSGRDALLDQIRQGIQLKSVSDGQESTPPTPAPTSGIVGALMEVMQKRSKAIHS
SDEDEDDDDEEDFEDDDEWED

Ligands and cofactors

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

Primary citation

Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism. Zimmet, A., Van Eeuwen, T., Boczkowska, M. et al. Sci Adv (2020) 6:eaaz7651-eaaz7651. DOI 10.1126/sciadv.aaz7651 · PubMed

Other PDB entries of the same protein (UniProt P61158 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I2B 3.0 Å, SPIN90-Arp2/3 nucleated bidirectional actin filaments
8P94 3.3 Å, Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches
6YW6 4.2 Å, Cryo-EM structure of the ARP2/3 1B5CL isoform complex.
6YW7 4.5 Å, Cryo-EM structure of the ARP2/3 1A5C isoform complex.

Browse structure collections

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