4JD2: Actin-related protein 3

Crystal structure of Bos taurus Arp2/3 complex binding with Mus musculus GMF. Determined by X-ray diffraction at 3.08 Å resolution. Released 17 Jul 2013.

Method: X-ray diffraction
Resolution: 3.08 Å
Organisms: Bos taurus, Mus musculus
Chains: 8
Atoms: 16,016
Mol. weight: 242.45 kDa
Ligands: CA, ATP
Released: 17 Jul 2013

Explore 4JD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JD2 contains 99 α-helices and 101 β-strands across 8 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: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
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	120-128	9
α-helix	129-133	5
β-strand	138-143	6	1
α-helix	144-151	8
α-helix	152-155	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	184-185	2	4
α-helix	187-189	3
β-strand	191-193	3	4
α-helix	197-211	15
α-helix	217-219	3
α-helix	220-231	12
β-strand	233	1	5
α-helix	238-247	10
β-strand	254-259	6	6
β-strand	266-271	6	6
α-helix	274-280	7
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
β-strand	329	1	5
α-helix	331-352	22
β-strand	367-368	2	4
α-helix	371-373	3
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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	7
β-strand	17-21	5	7
β-strand	30-33	4	7
β-strand	36-39	4	8
β-strand	56-57	2	8
α-helix	59-63	5
α-helix	65-67	3
β-strand	68-71	4	8
β-strand	74-75	2	9
β-strand	78-79	2	9
α-helix	82-93	12
α-helix	102-104	3
β-strand	106-111	6	7
α-helix	117-126	10
α-helix	127-131	5
β-strand	135-140	6	7
α-helix	141-147	7
β-strand	154-159	6	10
β-strand	164-170	7	10
β-strand	173-174	2	10
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	268-271	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	337-339	3
β-strand	344-345	2	10
α-helix	350-352	3
α-helix	353-364	12
β-strand	373-374	2	7
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	99-104	6	15
β-strand	110-115	6	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	166-170	5	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: 16 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	116-134	19
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
α-helix	196	1
β-strand	197-201	5	21
α-helix	214-216	3
β-strand	220-227	8	21
α-helix	229-232	4
α-helix	237-244	8
α-helix	247-278	32

Chain E: 9 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	123-148	26
β-strand	149-150	2	24
β-strand	155-156	2	24
α-helix	157	1
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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	16-19	4
α-helix	39-48	10
α-helix	51-58	8
α-helix	69-85	17
α-helix	88-90	3
α-helix	91-97	7
α-helix	100-113	14
α-helix	121-146	26

Chain H: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	26
α-helix	12-22	11
β-strand	30-37	8	26
β-strand	42-50	9	26
α-helix	54-60	7
β-strand	67-72	6	26
β-strand	75-76	2	27
β-strand	82-83	2	27
β-strand	86-91	6	26
α-helix	98-115	18
β-strand	119-123	5	26
α-helix	126-128	3
α-helix	131-138	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 3	A	protein	418	Bos taurus	P61157 (AlphaFold model)
Actin-related 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
Glia maturation factor gamma	H	protein	142	Mus musculus	Q9ERL7

Sequence of entity 1 (A), FASTA

>4JD2_1 Actin-related protein 3 (chains A)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Sequence of entity 2 (B), FASTA

>4JD2_2 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Sequence of entity 3 (C), FASTA

>4JD2_3 Actin-related protein 2/3 complex subunit 1B (chains C)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDW
APDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVR
SLESALKDLKIV

Sequence of entity 4 (D), FASTA

>4JD2_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 5 (E), FASTA

>4JD2_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Sequence of entity 6 (F), FASTA

>4JD2_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>4JD2_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MSKNTVSSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H), FASTA

>4JD2_8 Glia maturation factor gamma (chains H)
MSDSLVVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLE
LPERQPRFVVYSYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAELTKV
FEIRTTDDLTETWLKEKLAFFR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Water and common crystallization additives (PG4) are not listed.

Primary citation

Structural basis for regulation of Arp2/3 complex by GMF. Luan, Q., Nolen, B.J. Nat Struct Mol Biol (2013) 20:1062-1068. DOI 10.1038/nsmb.2628 · PubMed

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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