5nbn

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80

Method: X-RAY DIFFRACTION D_max: 179.6 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–489	Not recorded	Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–489	Not recorded	Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） 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

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 5NBN	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
5I9E Crystal structure of a nuclear actin ternary complex Deposited 2016-02-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–489（489 aa）	Not recorded	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
5I9E Crystal structure of a nuclear actin ternary complex Deposited 2016-02-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–489（489 aa）	Not recorded	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
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02	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 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 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 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
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 ligand/ion 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 1–489； UniProt 1–489 Author chain B； PDBConstruct 1–489； UniProt 1–489

Actin

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P60010

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–375	Non-standard monomer：Yes (specific site not provided by mmCIF)	Actin-related protein 4 × 1 （P80428） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–375	Non-standard monomer：Yes (specific site not provided by mmCIF)	Actin-related protein 4 × 1 （P80428） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5NBN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YAG STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX Deposited 1998-10-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–375（375 aa）	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.90 Å R-free 0.231
1YAG STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX Deposited 1998-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–375（375 aa）	Not recorded	MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.90 Å R-free 0.231
1YVN THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1. Deposited 1999-03-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–375（375 aa）	Mutation：V159N	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0.	Resolution 2.10 Å R-free 0.235
1YVN THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1. Deposited 1999-03-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–375（375 aa）	Mutation：V159N	MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0.	Resolution 2.10 Å R-free 0.235
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–375（375 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–375（375 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–375（375 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–375（375 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
5Y81 NuA4 TEEAA sub-complex Deposited 2017-08-18	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 × 8 PDB declaration: octameric	Chain G 1–375（375 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 mutation/modification 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 G 1–375（375 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 mutation/modification 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 G 1–375（375 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
7YFN Core module of the NuA4 complex in S. cerevisiae Deposited 2022-07-08	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 × 6 PDB declaration: hexameric	Chain A 4–375（372 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7YFP The NuA4 histone acetyltransferase complex from S. cerevisiae Deposited 2022-07-08	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 × 6 PDB declaration: hexameric	Chain A 4–375（372 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14	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 × 5 PDB declaration: pentameric	Chain V 1–375（375 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 mutation/modification 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 V 1–375（375 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 mutation/modification 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 A 1–375（375 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
9GO5 CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution. Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–375（375 aa） Chain B 1–375（375 aa） Chain C 1–375（375 aa） Chain D 1–375（375 aa） Chain E 1–375（375 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM Tris cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

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

Actin-like protein ARP8

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12386

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 255–881	Not recorded	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Putative DNA helicase INO80 × 1 （P53115） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 255–881	Not recorded	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Putative DNA helicase INO80 × 1 （P53115） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5NBN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4AM6 C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE Deposited 2012-03-07	Different construct 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 248–881（634 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；18% W/V PEG 5000 MME, 0.28 M LI2SO4, 0.1 M NA-CACODYLATE PH 6.5	Resolution 2.70 Å R-free 0.286
4AM6 C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE Deposited 2012-03-07	Different construct 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 248–881（634 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；18% W/V PEG 5000 MME, 0.28 M LI2SO4, 0.1 M NA-CACODYLATE PH 6.5	Resolution 2.70 Å R-free 0.286
4AM7 ADP-BOUND C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE Deposited 2012-03-07	Different construct 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 248–881（634 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；19.5% W/V PEG 5000 MME, 0.32 M LI2SO4, 0.1 M MES PH 6.5, 0.002 M ADP, 0.005 M MGCL2	Resolution 3.25 Å R-free 0.284
4AM7 ADP-BOUND C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE Deposited 2012-03-07	Different construct 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 248–881（634 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；19.5% W/V PEG 5000 MME, 0.32 M LI2SO4, 0.1 M MES PH 6.5, 0.002 M ADP, 0.005 M MGCL2	Resolution 3.25 Å R-free 0.284
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14	Different construct 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 U 1–881（881 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 construct 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 U 1–881（881 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

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARP8_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 2–628； UniProt 255–881 Author chain F； PDBConstruct 2–628； UniProt 255–881

Putative DNA helicase INO80

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P53115

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 462–598	Not recorded	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain G； UniProt 462–598	Not recorded	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5NBN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14	Different construct 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 G 1–598（598 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 construct 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 G 1–598（598 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
8ETS Class1 of the INO80-Hexasome complex Deposited 2022-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 948–1432（485 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.04 Å
8ETU Class2 of the INO80-Hexasome complex Deposited 2022-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 948–1432（485 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 2.80 Å
8ETW Class3 of INO80-Hexasome complex Deposited 2022-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 948–1432（485 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 2.64 Å
8EU9 Class1 of the INO80-Nucleosome complex Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 948–1440（493 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.48 Å
8EUF Class2 of the INO80-Nucleosome complex Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.41 Å
9C9G S.c INO80 in complex with S.c 0/80 nucleosome Deposited 2024-06-13	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: 20-meric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 2.91 Å
9C9S S.c INO80 in complex with S.c 0/40 nucleosome, Class 1 Deposited 2024-06-15	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: 20-meric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.09 Å
9C9T S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Deposited 2024-06-15	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: 20-meric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.16 Å
9C9Z S.c INO80 in complex with Xenopus 0/80 nucleosome, INO80 Core Deposited 2024-06-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 2.55 Å
9CAN S.c INO80 in complex with Xenopus 0/40 nucleosome Deposited 2024-06-17	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: 20-meric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.30 Å
9CAT DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module Deposited 2024-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 2.90 Å
9CB7 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Deposited 2024-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain Q 1–1489（1489 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 4.04 Å
9CCD DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module Deposited 2024-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.01 Å
9OB1 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Deposited 2025-04-21	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 Q 1–1489（1489 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	INO80_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 2–138； UniProt 462–598 Author chain H； PDBConstruct 2–138； UniProt 462–598

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	5nbn
Deposition date deposition_date	2017-03-02
Structure title title	Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80
Keywords keywords	Chromatin remodeling, Nanobody, INO80, SWR1, NuA4, 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	54.06 Å
Radius of gyration Rg (electron density) rg_electron	53.82 Å
Forward intensity I(0) i0	1515850000.00
Molecular weight molecular_weight	329710.0 kDa
Excluded volume excluded_volume	413940 Å³
Envelope volume envelope_volume	593840 Å³
Hydration-shell volume shell_volume	90062 Å³
Envelope diameter envelope_diameter	182.3 Å
Shell Rg shell_rg	58.04 Å
Envelope Rg envelope_rg	53.09 Å
Shape Rg shape_rg	53.81 Å
Total Rg total_rg	53.98 Å
Total atoms total_atoms	23215
Residues n_residues	2896
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	179.6 Å
Rg (real space) rg_real	53.97 Å
Rg uncertainty (real space) rg_real_error	1.81 Å
I(0) (real space) i0_real	1.5160e+09
I(0) uncertainty (real space) i0_real_error	2.9510e+07
Rg (reciprocal space) rg_reciprocal	54.11 Å
I(0) (reciprocal space) i0_reciprocal	1516000000.0000
Solution quality estimate total_estimate	0.8888
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	74.3 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.575
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	167300000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.836

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Actin-related protein 4
Molecular weight formula_weight	54894.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	23215

MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDIPANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSADTPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGVERLLNDRFR

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Actin
Molecular weight formula_weight	41748.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQSKRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSYELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYDESGPSIVHHKCF

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	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Actin-like protein ARP8
Molecular weight formula_weight	71987.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPLNDEIDLNDPTATIVIHPGSNSIKIGFPKDDHPVVVPNCVAVPKKWLDLENSEHVENVCLQREQSEEFNNIKSEMEKNFRERMRYYKRKVPGNAHEQVVSFNENSKPEIISEKNDPSPIEWIFDDSKLYYGSDALRCVDEKFVIRKPFRGGSFNVKSPYYKSLAELISDVTKLLEHALNSETLNVKPTKFNQYKVVLVIPDIFKKSHVETFIRVLLTELQFQAVAIIQESLATCYGAGISTSTCVVNIGAAETRIACVDEGTVLEHSAITLDYGGDDITRLFALFLLQSDFPLQDWKIDSKHGWLLAERLKKNFTTFQDADVAVQLYNFMNRSPNQPTEKYEFKLFDEVMLAPLALFFPQIFKLIRTSSHKNSSLEFQLPESRDLFTNELNDWNSLSQFESKEGNLYCDLNDDLKILNRILDAHNIIDQLQDKPENYGNTLKENFAPLEKAIVQSIANASITADVTRMNSFYSNILIVGGSSKIPALDFILTDRINIWRPSLLSSASFPQFYKKLTKEIKDLEGHYVNAPDKTEDENKQILQAQIKEKIVEELEEQHQNIEHQNGNEHIFPVSIIPPPRDMNPALIIWKGASVLAQIKLVEELFITNSDWDVHGSRILQYKCIFTY

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	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Putative DNA helicase INO80
Molecular weight formula_weight	18020.7 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	G,H

MARAIQRHYDNTYTTIWKDMARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMSNFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKNWSHPQFEK

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	Trichoplusia ni

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	LATRUNCULIN A
Molecular weight formula_weight	421.6 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	5nbnA01
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	5nbnA02
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	5nbnA03
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	5nbnB01
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	5nbnB02
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	5nbnB03
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	5nbnC01
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	5nbnC02
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	5nbnC03
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	5nbnD01
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	5nbnD02
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	5nbnD03
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	5nbnE01
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	5nbnE02
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	5nbnE03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	580 —

Domain ID domain_id	5nbnF01
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	5nbnF02
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	5nbnF03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	580 —

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8. Citations (1)

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Unit-cell length a length_a	172.294 Å
Unit-cell length b length_b	263.909 Å
Unit-cell length c length_c	241.402 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	49.399 Å
R factor r_factor	0.1953
R_work r_work	0.1927
R_free r_free	0.2422

fit	/app/data/saxs_computation/nb/5nbn/5nbn.fit
pddf	/app/data/pr_computation/nb/5nbn/5nbn.pr.out
profile	/app/data/saxs_computation/nb/5nbn/5nbn.dat

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80

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

Actin-like protein ARP8

State in the Current Structure

Other States of the Same Protein in the Database

Putative DNA helicase INO80

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 (7)

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 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)