1u2v

Crystal structure of Arp2/3 complex with bound ADP and calcium

Method: X-RAY DIFFRACTION D_max: 142.4 Å Quality: EXCELLENT

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–418	Not recorded	Actin-Related Protein 2 × 1 Arp2/3 Complex 41Kda Subunit × 1 Arp2/3 Complex 34Kda Subunit × 1 Arp2/3 Complex 21Kda Subunit × 1 Arp2/3 Complex 20Kda Subunit × 1 Arp2/3 Complex 16kDa Subunit × 1 CA CALCIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Hepes, potassium thiocyanate, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.55 Å R-free 0.258
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–418	Not recorded	Actin-Related Protein 2 × 1 Arp2/3 Complex 41Kda Subunit × 1 Arp2/3 Complex 34Kda Subunit × 1 Arp2/3 Complex 21Kda Subunit × 1 Arp2/3 Complex 20Kda Subunit × 1 Arp2/3 Complex 16kDa Subunit × 1 CA CALCIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Hepes, potassium thiocyanate, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.55 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1U2V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1K8K Crystal Structure of Arp2/3 Complex Deposited 2001-10-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 8000, KSCN, Hepes at pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.251
1TYQ Crystal structure of Arp2/3 complex with bound ATP and calcium Deposited 2004-07-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 8000, potassium thiocyanate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.55 Å R-free 0.272
2P9I Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with gluteraldehyde Deposited 2007-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；7.5% PEG 3350 50mM HEPES 100mM KSCN 10% Sucrose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.46 Å R-free 0.261
2P9K Crystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with glutaraldehyde Deposited 2007-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；7.5% PEG 3350, 50mM HEPES, 100mM KSCN, 10% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.59 Å R-free 0.260
2P9L Crystal Structure of bovine Arp2/3 complex Deposited 2007-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7.5% PEG3350 50mM HEPES 100mM KSCN 10% Sucrose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.266
2P9N Crystal Structure of bovine Arp2/3 complex co-crystallized with ADP Deposited 2007-03-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；6% PEG 8000 100mM HEPES 100mM KSCN, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.85 Å R-free 0.272
2P9P Crystal Structure of bovine Arp2/3 complex co-crystallized with ADP Deposited 2007-03-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7.5% PEG 3350 50mM HEPES 100mM KSCN 10% Sucrose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.288
2P9S Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+ Deposited 2007-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7.5% PEG3350 50mM HEPES 100mM KSCN 10% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.68 Å R-free 0.261
2P9U Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium Deposited 2007-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7.5% PEG3350 50mM HEPES 100mM KSCN 10% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.75 Å R-free 0.265
3DXK Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636 Deposited 2008-07-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	N23 N-[2-(2-methyl-1H-indol-3-yl)ethyl]thiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；8% PEG 8000, 50 mM HEPES, pH 7.5, 100 mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.262
3DXM Structure of Bos taurus Arp2/3 Complex with Bound Inhibitor CK0993548 Deposited 2008-07-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	N24 (2S)-2-(3-bromophenyl)-3-(5-chloro-2-hydroxyphenyl)-1,3-thiazolidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；8% PEG 8000, 50 mM HEPES, pH 7.5,100 mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.258
3RSE Structural and biochemical characterization of two binding sites for nucleation promoting factor WASp-VCA on Arp2/3 complex Deposited 2011-05-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–418（418 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100 mM HEPES 7.5, 8% PEG 8000, 200 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.65 Å R-free 0.259
3UKR Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666 Deposited 2011-11-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	CKH 2-fluoro-N-[2-(2-methyl-1H-indol-3-yl)ethyl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Hepes (pH 7.5), 0.2M KSCN, 16% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 Å R-free 0.261
3UKU Structure of Arp2/3 complex with bound inhibitor CK-869 Deposited 2011-11-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	C69 (2S)-2-(3-bromophenyl)-3-(2,4-dimethoxyphenyl)-1,3-thiazolidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；8% PEG 8000, 50 mM HEPES, pH 7.5, 100 mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.75 Å R-free 0.301
3ULE Structure of Bos taurus Arp2/3 complex with bound inhibitor CK-869 and ATP Deposited 2011-11-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 C69 (2S)-2-(3-bromophenyl)-3-(2,4-dimethoxyphenyl)-1,3-thiazolidin-4-one × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；277 K；8% PEG 8000, 50 mM HEPES, pH 7.5,100 mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.274
4JD2 Crystal structure of Bos taurus Arp2/3 complex binding with Mus musculus GMF Deposited 2013-02-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.08 Å R-free 0.248
4XEI Orthorhombic isomorph of bovine Arp2/3 complex Deposited 2014-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；Ethanol 10%, 1,4-butanediol 15%, 100 mM Tris 7.4	Resolution 3.87 Å R-free 0.329
4XF2 Tetragonal structure of Arp2/3 complex Deposited 2014-12-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–418（418 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM Tris 7.0, 15% ethanol	Resolution 5.00 Å R-free 0.303
4XF2 Tetragonal structure of Arp2/3 complex Deposited 2014-12-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain T 1–418（418 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM Tris 7.0, 15% ethanol	Resolution 5.00 Å R-free 0.303
6DEC Crystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90 Deposited 2018-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM HEPES, pH 7.5, 5% PEG3350, 50 mM L-Proline, 0.5 mM ATP, 0.5 mM calcium chloride, 1 mM DTT	Resolution 4.60 Å R-free 0.314
6DEC Crystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90 Deposited 2018-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–418（418 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM HEPES, pH 7.5, 5% PEG3350, 50 mM L-Proline, 0.5 mM ATP, 0.5 mM calcium chloride, 1 mM DTT	Resolution 4.60 Å R-free 0.314
7JPN Cryo-EM structure of Arpin-bound Arp2/3 complex Deposited 2020-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 3–415（413 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger.	Resolution 3.24 Å
7T5Q Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation Deposited 2021-12-13	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–418（418 aa）	Not recorded	MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger.	Resolution 3.40 Å
7TPT Single-particle Cryo-EM structure of Arp2/3 complex at branched-actin junction. Deposited 2022-01-26	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 1–418（418 aa）	Not recorded	MG MAGNESIUM ION × 16 ADP ADENOSINE-5'-DIPHOSPHATE × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8TAH Cryo-EM structure of Cortactin-bound to Arp2/3 complex Deposited 2023-06-27	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–418（418 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7；10 mM imidazole pH 7.0, 50 mM KCl, 2 mM MgCl2, 1 mM EGTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9DLX Bovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1 Deposited 2024-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 3–414（412 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
9DLZ Bovine Arp2/3 complex with N-WASP CA bound to Arp3 Deposited 2024-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 3–413（411 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9EAM Coronin-7 CA bound to Arp2/3 complex Deposited 2024-11-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–418（418 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9M5E Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex) Deposited 2025-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–418（418 aa）	Not recorded	MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
9M64 Structure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filaments (Doublet Complex) Deposited 2025-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–418（418 aa） Chain a 1–418（418 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 12 MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

28 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARP3_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–418； UniProt 1–418

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1u2v
Deposition date deposition_date	2004-07-20
Structure title title	Crystal structure of Arp2/3 complex with bound ADP and calcium
Keywords keywords	STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.81 Å
Radius of gyration Rg (electron density) rg_electron	43.43 Å
Forward intensity I(0) i0	538819000.00
Molecular weight molecular_weight	193300.0 kDa
Excluded volume excluded_volume	242800 Å³
Envelope volume envelope_volume	330560 Å³
Hydration-shell volume shell_volume	63039 Å³
Envelope diameter envelope_diameter	149.9 Å
Shell Rg shell_rg	48.68 Å
Envelope Rg envelope_rg	43.00 Å
Shape Rg shape_rg	43.43 Å
Total Rg total_rg	43.65 Å
Total atoms total_atoms	13608
Residues n_residues	1714
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	142.4 Å
Rg (real space) rg_real	43.76 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	5.3880e+08
I(0) uncertainty (real space) i0_real_error	9.4870e+06
Rg (reciprocal space) rg_reciprocal	43.81 Å
I(0) (reciprocal space) i0_reciprocal	538800000.0000
Solution quality estimate total_estimate	0.9002
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.5 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.682
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	77320000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.914

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Actin-Related Protein 3
Molecular weight formula_weight	47428.0 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	13922

MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Entity 2 Entity 2 polymer

Description description	Actin-Related Protein 2
Molecular weight formula_weight	44818.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Entity 3 Entity 3 polymer

Description description	Arp2/3 Complex 41Kda Subunit
Molecular weight formula_weight	41016.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGVDWAPDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARERFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVRSLESALKDLKIV

Entity 4 Entity 4 polymer

Description description	Arp2/3 Complex 34Kda Subunit
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	Arp2/3 Complex 21Kda Subunit
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	Arp2/3 Complex 20Kda Subunit
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	Arp2/3 Complex 16kDa Subunit
Molecular weight formula_weight	16295.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSKNTVSSARFRKVDVDEYDENKFVDEDDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Entity 8 Entity 8 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	314

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7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1u2va1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

Domain ID domain_id	d1u2va2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

Domain ID domain_id	d1u2vb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.1 — Actin/HSP70

Domain ID domain_id	d1u2vc_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.1 — WD40-repeat

Domain ID domain_id	d1u2vd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.2 — Arp2/3 complex subunits
Family Family family	d.198.2.1 — Arp2/3 complex subunits

Domain ID domain_id	d1u2vd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.2 — Arp2/3 complex subunits
Family Family family	d.198.2.1 — Arp2/3 complex subunits

Domain ID domain_id	d1u2ve_
Class class	a — All alpha proteins
Fold Fold fold	a.148 — Arp2/3 complex 21 kDa subunit ARPC3
Superfamily Superfamily superfamily	a.148.1 — Arp2/3 complex 21 kDa subunit ARPC3
Family Family family	a.148.1.1 — Arp2/3 complex 21 kDa subunit ARPC3

Domain ID domain_id	d1u2vf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.2 — Arp2/3 complex subunits
Family Family family	d.198.2.1 — Arp2/3 complex subunits

Domain ID domain_id	d1u2vg_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.13 — Arp2/3 complex 16 kDa subunit ARPC5
Family Family family	a.118.13.1 — Arp2/3 complex 16 kDa subunit ARPC5

CATH v4.4 (12 domains)

Domain ID domain_id	1u2vA01
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	1u2vA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	36 — Actin; Chain A, domain 2
Homologous superfamily homologous superfamily	70 — Actin; Chain A, domain 2

Domain ID domain_id	1u2vA03
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	1u2vA04
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	1u2vB01
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	1u2vB02
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	1u2vC00
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	1u2vD01
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	1u2vD02
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	1u2vE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1760 — Arp2/3 complex 21 kDa subunit ARPC3
Homologous superfamily homologous superfamily	10 — Actin-related protein 2/3 complex subunit 3

Domain ID domain_id	1u2vF00
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	1u2vG00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	111.300 Å
Unit-cell length b length_b	129.300 Å
Unit-cell length c length_c	204.700 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2250
R_work r_work	0.2230
R_free r_free	0.2580

fit	/app/data/saxs_computation/u2/1u2v/1u2v.fit
pddf	/app/data/pr_computation/u2/1u2v/1u2v.pr.out
profile	/app/data/saxs_computation/u2/1u2v/1u2v.dat

Crystal structure of Arp2/3 complex with bound ADP and calcium

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (10)

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 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)