9I2B: Actin-related protein 2

SPIN90-Arp2/3 nucleated bidirectional actin filaments. Determined by electron microscopy at 3.0 Å resolution. Released 3 Sept 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Sus scrofa, Amanita phalloides
Chains: 24
Atoms: 48,862
Mol. weight: 781.83 kDa
Ligands: MG, ADP
Released: 3 Sept 2025

Explore 9I2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I2B contains 350 α-helices and 282 β-strands across 24 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.

Chains A and K: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8-12	5	36
β-strand	16-21	6	36
β-strand	29-32	4	36
β-strand	35-38	4	37
α-helix	56-58	3
β-strand	60-62	3	37
α-helix	64-67	4
β-strand	72-75	4	37
β-strand	78-79	2	38
β-strand	82-83	2	38
α-helix	86-95	10
α-helix	96-101	6
β-strand	110-114	5	36
α-helix	120-128	9
α-helix	129-133	5
β-strand	138-139	2	39
β-strand	140-143	4	36
α-helix	144-155	12
α-helix	157	1
β-strand	165-170	6	40
β-strand	175-181	7	40
β-strand	184-185	2	40
α-helix	187-189	3
β-strand	191-193	3	40
α-helix	197-211	15
α-helix	217-219	3
α-helix	220-230	11
α-helix	238-247	10
α-helix	249-252	4
β-strand	254-259	6	41
β-strand	266-271	6	41
α-helix	273-275	3
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	40
α-helix	324-326	3
α-helix	332-354	23
α-helix	360-363	4
β-strand	367-369	3	40
α-helix	376-385	10
α-helix	390-393	4
β-strand	395-396	2	39
α-helix	397-403	7
α-helix	405-408	4

Chains B and L: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	17-22	6	1
β-strand	30-33	4	1
β-strand	36-39	4	2
β-strand	40-42	3	3
β-strand	56-57	2	2
α-helix	59-62	4
α-helix	65-67	3
β-strand	68-71	4	2
β-strand	74-75	2	4
β-strand	78-79	2	4
α-helix	82-92	11
β-strand	94	1	5
β-strand	97	1	5
α-helix	102-104	3
β-strand	105-111	7	1
α-helix	118-129	12
β-strand	135-140	6	1
α-helix	141-149	9
β-strand	153	1	6
β-strand	156-159	4	7
β-strand	164-167	4	7
β-strand	169-170	2	6
β-strand	173-174	2	6
α-helix	176-178	3
β-strand	180-182	3	7
α-helix	186-197	12
α-helix	209-219	11
α-helix	227-236	10
β-strand	242-245	4	8
β-strand	251-254	4	8
α-helix	257-260	4
α-helix	262-265	4
α-helix	268-271	4
α-helix	278-286	9
α-helix	294-298	5
β-strand	301-304	4	7
α-helix	306-308	3
α-helix	313-324	12
α-helix	325-329	5
α-helix	335-339	5
β-strand	344-345	2	7
α-helix	353-365	13
β-strand	373-374	2	1
α-helix	375-380	6
α-helix	383-389	7

Chains c, d, U and V: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	20

Chains C and M: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	28
β-strand	16	1	29
β-strand	22-25	4	29
β-strand	32-38	7	29
β-strand	41-48	8	29
β-strand	55-60	6	30
β-strand	66-71	6	30
β-strand	76-82	7	30
β-strand	85-87	3	30
β-strand	90	1	30
β-strand	99-104	6	31
β-strand	111-115	5	31
β-strand	120-126	7	31
β-strand	131-136	6	31
β-strand	145-150	6	32
β-strand	156-161	6	32
β-strand	166-170	5	32
α-helix	178-182	5
β-strand	183	1	33
β-strand	186	1	33
β-strand	196	1	32
β-strand	205-210	6	34
β-strand	216-221	6	34
β-strand	225-230	6	34
β-strand	236-241	6	34
β-strand	247-252	6	35
β-strand	257-262	6	35
β-strand	267-273	7	35
β-strand	278-284	7	35
α-helix	287-289	3
β-strand	329-336	8	28
β-strand	344-349	6	28
β-strand	353-358	6	28
α-helix	359-365	7

Chains D and N: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-22	14
α-helix	26-28	3
β-strand	32-36	5	9
β-strand	42-46	5	9
α-helix	48-50	3
β-strand	54-55	2	10
β-strand	56-59	4	9
α-helix	65-68	4
α-helix	72-77	6
α-helix	81-83	3
α-helix	87-88	2
β-strand	93-94	2	9
β-strand	97-98	2	10
α-helix	102-103	2
α-helix	107-114	8
α-helix	116-133	18
α-helix	139-141	3
β-strand	142-147	6	11
β-strand	150-156	7	11
β-strand	161-168	8	11
α-helix	172-185	14
α-helix	186-189	4
α-helix	196	1
β-strand	197-201	5	11
β-strand	220-227	8	11
α-helix	229-232	4
α-helix	237-244	8
α-helix	247-277	31

Chains E and O: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	12
β-strand	19-21	3	12
β-strand	24	1	13
α-helix	33	1
β-strand	34	1	13
α-helix	35	1
α-helix	41-47	7
α-helix	49-52	4
β-strand	57-59	3	3
α-helix	64-82	19
α-helix	88-100	13
α-helix	123-148	26
β-strand	149-150	2	14
β-strand	155-156	2	14
α-helix	161-163	3

Chains F and P: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
α-helix	37-40	4
α-helix	44-46	3
β-strand	47-53	7	15
β-strand	60-66	7	15
β-strand	69-75	7	15
α-helix	81-95	15
β-strand	104	1	15
α-helix	108-109	2
β-strand	114-119	6	15
α-helix	120-125	6
α-helix	128-165	38

Chains G and Q: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	9-11	3
α-helix	29-33	5
α-helix	41-49	9
α-helix	53-62	10
α-helix	72-86	15
α-helix	93-97	5
α-helix	102-115	14
α-helix	124-138	15
α-helix	140-147	8

3 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 2	B, L	protein	394	Homo sapiens	P61160 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D, N	protein	300	Homo sapiens	O15144 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E, O	protein	178	Homo sapiens	O15145 (AlphaFold model)
Actin-related protein 2/3 complex subunit 4	F, P	protein	168	Homo sapiens	P59998 (AlphaFold model)
Actin-related protein 2/3 complex subunit 5-like protein	G, Q	protein	153	Homo sapiens	Q9BPX5
Actin, cytoplasmic 1	I, J, S, T	protein	375	Sus scrofa	Q6QAQ1
Phalloidin	U, V, c, d	protein	7	Amanita phalloides
NCK-interacting protein with SH3 domain	H, R	protein	722	Homo sapiens	Q9NZQ3
Actin-related protein 2/3 complex subunit 1B	C, M	protein	372	Homo sapiens	O15143
Actin-related protein 3	A, K	protein	418	Homo sapiens	P61158

Sequence of entity 1 (B, L), FASTA

>9I2B_1 Actin-related protein 2 (chains B, L)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Sequence of entity 2 (D, N), FASTA

>9I2B_2 Actin-related protein 2/3 complex subunit 2 (chains D, N)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSFLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 3 (E, O), FASTA

>9I2B_3 Actin-related protein 2/3 complex subunit 3 (chains E, O)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Sequence of entity 4 (F, P), FASTA

>9I2B_4 Actin-related protein 2/3 complex subunit 4 (chains F, P)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 5 (G, Q), FASTA

>9I2B_5 Actin-related protein 2/3 complex subunit 5-like protein (chains G, Q)
MARNTLSSRFRRVDIDEFDENKFVDEQEEAAAAAAEPGPDPSEVDGLLRQGDMLRAFHAA
LRNSPVNTKNQAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGVDLLMKYIYKGFEKPT
ENSSAVLLQWHEKALAVGGLGSIIRVLTARKTV

Sequence of entity 6 (I, J, S, T), FASTA

>9I2B_6 Actin, cytoplasmic 1 (chains I, J, S, T)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Sequence of entity 7 (U, V, c, d), FASTA

>9I2B_7 Phalloidin (chains U, V, c, d)
WXATCPA

Sequence of entity 8 (H, R), FASTA

>9I2B_8 NCK-interacting protein with SH3 domain (chains H, R)
MYRALYAFRSAEPNALAFAAGETFLVLERSSAHWWLAARARSGETGYVPPAYLRRLQGLE
QDVLQAIDRAIEAVHNTAMRDGGKYSLEQRGVLQKLIHHRKETLSRRGPSASSVAVMTSS
TSDHHLDAAAARQPNGVCRAGFERQHSLPSSEHLGADGGLYQIPLPSSQIPPQPRRAAPT
TPPPPVKRRDREALMASGSGGHNTMPSGGNSVSSGSSVSSTSLDTLYTSSSPSEPGSSCS
PTPPPVPRRGTHTTVSQVQPPPSKASAPEPPAEEEVATGTTSASDDLEALGTLSLGTTEE
KAAAEAAVPRTIGAELMELVRRNTGLSHELCRVAIGIIVGHIQASVPASSPVMEQVLLSL
VEGKDLSMALPSGQVCHDQQRLEVIFADLARRKDDAQQRSWALYEDEGVIRCYLEELLHI
LTDADPEVCKKMCKRNEFESVLALVAYYQMEHRASLRLLLLKCFGAMCSLDAAIISTLVS
SVLPVELARDMQTDTQDHQKLCYSALILAMVFSMGEAVPYAHYEHLGTPFAQFLLNIVED
GLPLDTTEQLPDLCVNLLLALNLHLPAADQNVIMAALSKHANVKIFSEKLLLLLNRGDDP
VRIFKHEPQPPHSVLKFLQDVFGSPATAAIFYHTDMMALIDITVRHIADLSPGDKLRMEY
LSLMHAIVRTTPYLQHRHRLPDLQAILRRILNEEETSPQCQMDRMIVREMCKEFLVLGEA
PS

Sequence of entity 9 (C, M), FASTA

>9I2B_9 Actin-related protein 2/3 complex subunit 1B (chains C, M)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWTKVHELKEHNGQVTGIDW
APESNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSASGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLALTFITDNSLVAAGHDCFPVLFTYDAAAGMLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGGTAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVK
SLESALKDLKIK

Sequence of entity 10 (A, K), FASTA

>9I2B_10 Actin-related protein 3 (chains A, K)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	8

Primary citation

Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers. Liu, T., Cao, L., Mladenov, M. et al. Nat Struct Mol Biol (2025) 32:2262-2271. DOI 10.1038/s41594-025-01665-8 · PubMed

Other PDB entries of the same protein (UniProt P61160 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P94 3.3 Å, Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches
6UHC 3.9 Å, CryoEM structure of human Arp2/3 complex with bound NPFs
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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