3dwl

Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit

Method: X-RAY DIFFRACTION

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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 6	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） ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	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） 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 Author chain B； PDBConstruct 1–427； UniProt 1–427

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 6	Actin-related protein 3 × 1 （P32390） 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） ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Actin-related protein 3 × 1 （P32390） 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） 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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–377； UniProt 1–377 Author chain H； 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 6	Actin-related protein 3 × 1 （P32390） 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） ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Actin-related protein 3 × 1 （P32390） 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） 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	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–317； UniProt 1–317 Author chain I； 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 6	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 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	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 4 × 1 （Q92352） Actin-related protein 2/3 complex subunit 5 × 1 （Q10316） 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	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–174； UniProt 1–174 Author chain J； 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 6	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 5 × 1 （Q10316） ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	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 5 × 1 （Q10316） 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	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–168； UniProt 1–168 Author chain K； 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 6	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） ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	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） 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	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–152； UniProt 1–152 Author chain L； PDBConstruct 1–152； UniProt 1–152

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	3dwl
Deposition date deposition_date	2008-07-22
Structure title title	Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit
Keywords keywords	PROPELLOR, Actin-binding, ATP-binding, Cytoskeleton, Nucleotide-binding, WD repeat, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3dwl__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dwl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dwl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	42.12 Å
Rg (electron density)	41.62 Å
Total Rg	41.73 Å
Atom count	9358
Residues	1307
Excluded volume	163530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dwl__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dwl__assembly_2__model_1`	hexameric （6）	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 (7)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	18705

MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGSGHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCEPEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLTGTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERIKEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIASSDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHRSEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRYQIFGNSL

Entity 2 Entity 2 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTCVDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSGARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDVDAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQPPRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFTHTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNITAFTSSGTDGRVVLWTL

Entity 3 Entity 3 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYPELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLAAPFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVFSTKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGFVTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKPDVELERKTATGRSFVRA

Entity 4 Entity 4 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J

MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNFEIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAPPLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL

Entity 5 Entity 5 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,K

MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQCLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITNYHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF

Entity 6 Entity 6 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,L

MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLLSYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQAYNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL

Entity 7 Entity 7 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) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	3dwlA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3dwlA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3dwlA03
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	3dwlB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3dwlB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3dwlB03
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	3dwlC00
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	3dwlD01
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	3dwlD02
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	3dwlE00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	3dwlF00
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	3dwlG00
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

Domain ID domain_id	3dwlH00
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	3dwlI01
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	3dwlI02
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	3dwlJ00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	3dwlK00
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	3dwlL00
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	218.967 Å
Unit-cell length b length_b	218.967 Å
Unit-cell length c length_c	315.049 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	16

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	3.780 Å
Low-resolution limit resolution_low	29.000 Å
R factor r_factor	0.3247
R_work r_work	0.3237
R_free r_free	0.3437

Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit

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 2/3 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dwl__assembly_2__model_1

3dwl__assembly_2__model_1 | I(q)

3dwl__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)