5i9e

Crystal structure of a nuclear actin ternary complex

Method: X-RAY DIFFRACTION D_max: 138.0 Å Quality: GOOD

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

Actin-related protein 4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–489	Not recorded	Actin × 1 （P60011） Helicase SWR1 × 1 （Q05471） MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane	Resolution 2.80 Å R-free 0.284
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–489	Not recorded	Actin × 1 （P60011） Helicase SWR1 × 1 （Q05471） MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane	Resolution 2.80 Å R-free 0.284

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 5I9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–489（489 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.221
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–489（489 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.221
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–489（489 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.221
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–489（489 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.221
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–489（489 aa）	Not recorded	CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))	Resolution 2.80 Å R-free 0.204
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–489（489 aa）	Not recorded	CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))	Resolution 2.80 Å R-free 0.204
5NBM Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody Deposited 2017-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–489（489 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))	Resolution 3.40 Å R-free 0.193
5NBM Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody Deposited 2017-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–489（489 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))	Resolution 3.40 Å R-free 0.193
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–489（489 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)	Resolution 4.00 Å R-free 0.242
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–489（489 aa）	Not recorded	CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)	Resolution 4.00 Å R-free 0.242
5Y81 NuA4 TEEAA sub-complex Deposited 2017-08-18	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 F 1–489（489 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
7VVY TRA module of NuA4 Deposited 2021-11-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–489（489 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain F 1–489（489 aa）	Not recorded	CMC CARBOXYMETHYL COENZYME A × 1 MG MAGNESIUM ION × 2 ATP* ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 8.80 Å
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain W 1–489（489 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8A5O Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Deposited 2022-06-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain W 1–489（489 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8ESC Structure of the Yeast NuA4 Histone Acetyltransferase Complex Deposited 2022-10-13	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–489（489 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARP4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–490； UniProt 1–489 Author chain C； PDBConstruct 2–490； UniProt 1–489

Actin

Saccharomyces bayanus

UniProt P60011

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–375	Not recorded	Actin-related protein 4 × 1 （P80428） Helicase SWR1 × 1 （Q05471） MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane	Resolution 2.80 Å R-free 0.284
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–375	Not recorded	Actin-related protein 4 × 1 （P80428） Helicase SWR1 × 1 （Q05471） MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane	Resolution 2.80 Å R-free 0.284

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ACT_SACBA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–375； UniProt 1–375 Author chain D； PDBConstruct 1–375； UniProt 1–375

Helicase SWR1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q05471

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 340–410	Fragment：UNP residues 340-410	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60011） MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane	Resolution 2.80 Å R-free 0.284
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain H； UniProt 340–410	Fragment：UNP residues 340-410	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60011） MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane	Resolution 2.80 Å R-free 0.284

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5I9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4M6B Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer Deposited 2013-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 590–639（50 aa） Fragment：Swr1-Z domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% (w/v) PEG 2000 MME, 100 mM HEPES, pH 7.5, 50 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.78 Å R-free 0.220
4M6B Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer Deposited 2013-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 590–639（50 aa） Fragment：Swr1-Z domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% (w/v) PEG 2000 MME, 100 mM HEPES, pH 7.5, 50 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.78 Å R-free 0.220
6GEJ Chromatin remodeller-nucleosome complex at 3.6 A resolution. Deposited 2018-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GEN Chromatin remodeller-nucleosome complex at 4.5 A resolution. Deposited 2018-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8QKU SWR1-nucleosome complex in configuration 1 Deposited 2023-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8QKV SWR1-nucleosome complex in configuration 2 Deposited 2023-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
8QYV SWR1-hexasome complex Deposited 2023-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8QZ0 SWR1-hexasome-dimer complex Deposited 2023-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9FBW SWR1 lacking Swc5 subunit in complex with hexasome Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric	Chain M 1–1514（1514 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SWR1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–71； UniProt 340–410 Author chain H； PDBConstruct 1–71； UniProt 340–410

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	5i9e
Deposition date deposition_date	2016-02-20
Structure title title	Crystal structure of a nuclear actin ternary complex
Keywords keywords	nuclear actin, Arp4, chromatin remodeling, HYDROLASE; HYDROLASE
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	40.99 Å
Radius of gyration Rg (electron density) rg_electron	40.84 Å
Forward intensity I(0) i0	477943000.00
Molecular weight molecular_weight	179980.0 kDa
Excluded volume excluded_volume	225450 Å³
Envelope volume envelope_volume	298070 Å³
Hydration-shell volume shell_volume	60201 Å³
Envelope diameter envelope_diameter	143.7 Å
Shell Rg shell_rg	46.78 Å
Envelope Rg envelope_rg	40.80 Å
Shape Rg shape_rg	40.82 Å
Total Rg total_rg	41.18 Å
Total atoms total_atoms	12655
Residues n_residues	1599
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	138.0 Å
Rg (real space) rg_real	41.06 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	4.7790e+08
I(0) uncertainty (real space) i0_real_error	8.3930e+06
Rg (reciprocal space) rg_reciprocal	40.99 Å
I(0) (reciprocal space) i0_reciprocal	477900000.0000
Solution quality estimate total_estimate	0.8768
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.5 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	85550000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.887

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Actin-related protein 4
Molecular weight formula_weight	54991.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12666

PMSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDIPANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSADTPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGVERLLNDRFR

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Actin
Molecular weight formula_weight	41735.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQSKRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSYELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYDESGPSIVHHKCF

来源 Source

来源生物 organism	Saccharomyces bayanus
通用名 common_name	Yeast
NCBI Class编号 ncbi_taxonomy_id	4931
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Helicase SWR1
Molecular weight formula_weight	9224.5 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SYFYKQQDLQIHTDHLINQGIHMSKLFRSSTKARIARAKKVSQMIEQHFKHVAGAEERKAKEEERHKKSLAHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 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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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5i9eb1
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	d5i9eb2
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	d5i9ed1
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	d5i9ed2
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

CATH v4.4 (12 domains)

Domain ID domain_id	5i9eA01
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	5i9eA02
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	5i9eA03
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	5i9eB01
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	5i9eB02
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	5i9eB03
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	5i9eC01
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	5i9eC02
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	5i9eC03
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	5i9eD01
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	5i9eD02
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	5i9eD03
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

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8. Citations (1)

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Unit-cell length a length_a	110.260 Å
Unit-cell length b length_b	202.220 Å
Unit-cell length c length_c	87.010 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	48.403 Å
R factor r_factor	0.2338
R_work r_work	0.2317
R_free r_free	0.2844

fit	/app/data/saxs_computation/i9/5i9e/5i9e.fit
pddf	/app/data/pr_computation/i9/5i9e/5i9e.pr.out
profile	/app/data/saxs_computation/i9/5i9e/5i9e.dat

Crystal structure of a nuclear actin ternary complex

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

Actin-related protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Actin

State in the Current Structure

Other States of the Same Protein in the Database

Helicase SWR1

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)