7jpn

Cryo-EM structure of Arpin-bound Arp2/3 complex

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin-related protein 3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP3_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–413； UniProt 3–415

Actin-related protein 2

OrganismNot specified

UniProt A7MB62

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP2_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–377； UniProt 4–380

Actin-related protein 2/3 complex subunit 1B

OrganismNot specified

UniProt Q58CQ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARC1B_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–372； UniProt 1–372

Actin-related protein 2/3 complex subunit 2

OrganismNot specified

UniProt Q3MHR7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC2_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–300； UniProt 1–300

Actin-related protein 2/3 complex subunit 3

OrganismNot specified

UniProt Q3T035

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC3_BOVIN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–178； UniProt 1–178

Actin-related protein 2/3 complex subunit 4

OrganismNot specified

UniProt Q148J6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC4_BOVIN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–168； UniProt 1–168

Actin-related protein 2/3 complex subunit 5

OrganismNot specified

UniProt G3MXC8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Arpin × 1 （Q7Z6K5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3MXC8_BOVIN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–143； UniProt 9–151

Arpin

Homo sapiens

UniProt Q7Z6K5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Actin-related protein 3 × 1 （P61157） Actin-related protein 2 × 1 （A7MB62） Actin-related protein 2/3 complex subunit 1B × 1 （Q58CQ2） Actin-related protein 2/3 complex subunit 2 × 1 （Q3MHR7） Actin-related protein 2/3 complex subunit 3 × 1 （Q3T035） Actin-related protein 2/3 complex subunit 4 × 1 （Q148J6） Actin-related protein 2/3 complex subunit 5 × 1 （G3MXC8） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPIN_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–34； UniProt 193–226

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7jpn
Deposition date deposition_date	2020-08-09
Structure title title	Cryo-EM structure of Arpin-bound Arp2/3 complex
Keywords keywords	;actin, ATPase, actin related protein, arp, cytoskeleton, Arp2-3 complex, actin nucleation, actin branching, CONTRACTILE PROTEIN, Arpin ;; CONTRACTILE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7jpn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7jpn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7jpn__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.87 Å
Rg (electron density)	43.31 Å
Total Rg	43.57 Å
Atom count	15040
Residues	1885
Excluded volume	267850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7jpn__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Actin-related protein 3
Molecular weight formula_weight	46908.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	15040

GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFG

Entity 2 Entity 2 polymer

Description description	Actin-related protein 2
Molecular weight formula_weight	42945.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQE

Entity 3 Entity 3 polymer

Description description	Actin-related protein 2/3 complex subunit 1B
Molecular weight formula_weight	41030.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDWAPDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARERFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVRSLESALKDLKIV

Entity 4 Entity 4 polymer

Description description	Actin-related protein 2/3 complex subunit 2
Molecular weight formula_weight	34402.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSISLKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKVFMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNTINLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Entity 5 Entity 5 polymer

Description description	Actin-related protein 2/3 complex subunit 3
Molecular weight formula_weight	20572.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Entity 6 Entity 6 polymer

Description description	Actin-related protein 2/3 complex subunit 4
Molecular weight formula_weight	19697.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEKVLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITNFHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Entity 7 Entity 7 polymer

Description description	Actin-related protein 2/3 complex subunit 5
Molecular weight formula_weight	15473.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

ARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Entity 8 Entity 8 polymer

Description description	Arpin
Molecular weight formula_weight	3730.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

ASWTDNIMAQKCSKGAAAEIREQGDGAEDEEWDD

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7jpnA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

Domain ID domain_id	7jpnC01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.24 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	182324

Cryo-EM structure of Arpin-bound Arp2/3 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin-related protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 2/3 complex subunit 1B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 2/3 complex subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 2/3 complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 2/3 complex subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 2/3 complex subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Arpin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7jpn__assembly_1__model_1

7jpn__assembly_1__model_1 | I(q)

7jpn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer