8e9b

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction

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 15	Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP3_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–427； UniProt 1–427

Actin-related protein 2

OrganismNot specified

UniProt Q9UUJ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP2_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–390； UniProt 1–390

Actin-related protein 2/3 complex subunit 1

OrganismNot specified

UniProt P78774

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC1_SCHPO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–377； UniProt 1–377

Actin-related protein 2/3 complex subunit 2

OrganismNot specified

UniProt O14241

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC2_SCHPO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–317； UniProt 1–317

Actin-related protein 2/3 complex subunit 3

OrganismNot specified

UniProt Q9Y7J4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC3_SCHPO
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–174； UniProt 1–174

Actin-related protein 2/3 complex subunit 4

OrganismNot specified

UniProt Q92352

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC4_SCHPO
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 Q10316

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin, alpha skeletal muscle × 8 （P68139） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARPC5_SCHPO
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–152； UniProt 1–152

Actin, alpha skeletal muscle

OrganismNot specified

UniProt P68139

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Actin-related protein 3 × 1 （P32390） Actin-related protein 2 × 1 （Q9UUJ1） Actin-related protein 2/3 complex subunit 1 × 1 （P78774） Actin-related protein 2/3 complex subunit 2 × 1 （O14241） Actin-related protein 2/3 complex subunit 3 × 1 （Q9Y7J4） Actin-related protein 2/3 complex subunit 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） MAGNESIUM ION × 10 ADENOSINE-5'-DIPHOSPHATE × 9 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACTS_CHICK
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–375； UniProt 3–377 Author chain I； PDBConstruct 1–375； UniProt 3–377 Author chain M； PDBConstruct 1–375； UniProt 3–377 Author chain N； PDBConstruct 1–375； UniProt 3–377 Author chain O； PDBConstruct 1–375； UniProt 3–377 Author chain P； PDBConstruct 1–375； UniProt 3–377 Author chain Q； PDBConstruct 1–375； UniProt 3–377 Author chain R； PDBConstruct 1–375； UniProt 3–377

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	8e9b
Deposition date deposition_date	2022-08-26
Last revision last_revision	2023-02-01
Structure title title	Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction
Keywords keywords	Arp2-3 complex, branch juction, polymerization, STRUCTURAL PROTEIN; STRUCTURAL 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.

8e9b__assembly_1__model_1

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

Download this curve (.dat)

8e9b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8e9b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	63.06 Å
Rg (electron density)	63.13 Å
Total Rg	63.21 Å
Atom count	39160
Residues	4925
Excluded volume	696250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8e9b__assembly_1__model_1`	pentadecameric （15）	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 (11)

Entity 1 Entity 1 polymer

Description description	Actin-related protein 3
Molecular weight formula_weight	47427.1 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	39160

MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGSGHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCEPEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLTGTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERIKEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIASSDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHRSEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRYQIFGNSL

Entity 2 Entity 2 polymer

Description description	Actin-related protein 2
Molecular weight formula_weight	44286.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEAVRSLLQVKYPMENGIIRDFEEMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMCETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVTHIVPVYESVVLNHLVGRLDVAGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNYTLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLSGGSSMYAGLPSRLEKEIKQLWFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADIMAQNDHMWVSKAEWEEYGVRALDKLGPRTT

Entity 3 Entity 3 polymer

Description description	Actin-related protein 2/3 complex subunit 1
Molecular weight formula_weight	41643.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTCVDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSGARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDVDAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQPPRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFTHTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNITAFTSSGTDGRVVLWTL

Entity 4 Entity 4 polymer

Description description	Actin-related protein 2/3 complex subunit 2
Molecular weight formula_weight	37025.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYPELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLAAPFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVFSTKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGFVTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKPDVELERKTATGRSFVRA

Entity 5 Entity 5 polymer

Description description	Actin-related protein 2/3 complex subunit 3
Molecular weight formula_weight	19865.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNFEIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAPPLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL

Entity 6 Entity 6 polymer

Description description	Actin-related protein 2/3 complex subunit 4
Molecular weight formula_weight	19637.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQCLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITNYHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF

Entity 7 Entity 7 polymer

Description description	Actin-related protein 2/3 complex subunit 5
Molecular weight formula_weight	16922.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLLSYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQAYNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL

Entity 8 Entity 8 polymer

Description description	Actin, alpha skeletal muscle
Molecular weight formula_weight	41875.6 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R,H,I

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

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	10

Entity 10 Entity 10 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 11 Entity 11 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	8e9bA01
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	8e9bB01
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	8e9bC01
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

Domain ID domain_id	8e9bD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	8e9bG01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	190 — Actin-related protein 2/3 complex subunit 5

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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	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	79467

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction

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 1

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

Actin, alpha skeletal muscle

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

8e9b__assembly_1__model_1

8e9b__assembly_1__model_1 | I(q)

8e9b__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer