9ccd

DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module

Method: ELECTRON MICROSCOPY

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

Chromatin-remodeling ATPase INO80

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Actin-related protein 5 × 1 （P53946） Chromatin-remodeling complex subunit IES6 × 1 （P32617） RuvB-like protein 1 × 3 （Q03940） RuvB-like protein 2 × 3 （Q12464） Ino eighty subunit 2 × 1 （P40154） ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	INO80_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Q； PDBConstruct 1–1489； UniProt 1–1489

Actin-related protein 5

OrganismNot specified

UniProt P53946

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Chromatin-remodeling ATPase INO80 × 1 （P53115） Chromatin-remodeling complex subunit IES6 × 1 （P32617） RuvB-like protein 1 × 3 （Q03940） RuvB-like protein 2 × 3 （Q12464） Ino eighty subunit 2 × 1 （P40154） ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP5_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 1–755； UniProt 1–755

Chromatin-remodeling complex subunit IES6

OrganismNot specified

UniProt P32617

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-related protein 5 × 1 （P53946） RuvB-like protein 1 × 3 （Q03940） RuvB-like protein 2 × 3 （Q12464） Ino eighty subunit 2 × 1 （P40154） ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IES6_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain S； PDBConstruct 1–166； UniProt 1–166

RuvB-like protein 1

OrganismNot specified

UniProt Q03940

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-related protein 5 × 1 （P53946） Chromatin-remodeling complex subunit IES6 × 1 （P32617） RuvB-like protein 2 × 3 （Q12464） Ino eighty subunit 2 × 1 （P40154） ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUVB1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain T； PDBConstruct 1–463； UniProt 1–463 Author chain V； PDBConstruct 1–463； UniProt 1–463 Author chain X； PDBConstruct 1–463； UniProt 1–463

RuvB-like protein 2

OrganismNot specified

UniProt Q12464

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-related protein 5 × 1 （P53946） Chromatin-remodeling complex subunit IES6 × 1 （P32617） RuvB-like protein 1 × 3 （Q03940） Ino eighty subunit 2 × 1 （P40154） ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUVB2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain U； PDBConstruct 1–460； UniProt 1–460 Author chain W； PDBConstruct 1–460； UniProt 1–460 Author chain Y； PDBConstruct 1–460； UniProt 1–460

Ino eighty subunit 2

OrganismNot specified

UniProt P40154

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-related protein 5 × 1 （P53946） Chromatin-remodeling complex subunit IES6 × 1 （P32617） RuvB-like protein 1 × 3 （Q03940） RuvB-like protein 2 × 3 （Q12464） ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IES2_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain Z； PDBConstruct 1–320； UniProt 1–320

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ccd
Deposition date deposition_date	2024-06-21
Structure title title	DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module
Keywords keywords	Chromatin Remodeler, nucleosome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9ccd__assembly_1__model_1

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

Download this curve (.dat)

9ccd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ccd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.73 Å
Rg (electron density)	51.55 Å
Total Rg	51.50 Å
Atom count	27123
Residues	3472
Excluded volume	484970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ccd__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Chromatin-remodeling ATPase INO80
Molecular weight formula_weight	171693.8 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q
Atom count atom_count	27123

MSLAVLLNKEDKDISDFSKTTAGKSAKKNSRERVADVAPTRVLDKKQAYLSQLNSEFNRIKRRDSIEQLYQDWKFINLQEFELISEWNQQSKDWQFDNTNDSQDLHFKKLYRDMSMINKEWAEYQSFKNANLSDIINEKDADEDEEDDEDELEDGEEDMEEDEASTGRHTNGKSMRGNGIQKSRKKDAAAAAAIGKAIKDDQTHADTVVTVNGDENEDGNNGEDEDNDNDNENNNDNDNDNENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDFNPDVEKRRKRSSSSSSSTKLSMNSLSLITSKKINKNITINSDRPKIVRELIKMCNKNKHQKIKKRRFTNCIVTDYNPIDSKLNIKITLKQYHVKRLKKLINDAKREREREEALKNNVGLDGNDLDNDEDGSESHKRRKLNNNTANGADDANKRKFNTRHGLPTYGMKMNAKEARAIQRHYDNTYTTIWKDMARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMSNFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKIKTNELEGNNVSSNDSESQKNIDISALAPNKNDFHAIDFDNENDEQLRLRAAENASNALAETRAKAKQFDDHANAHEEEEEEDELNFQNPTSLGEITIEQPKILACTLKEYQLKGLNWLANLYDQGINGILADEMGLGKTVQSISVLAHLAENHNIWGPFLVVTPASTLHNWVNEISKFLPQFKILPYWGNANDRKVLRKFWDRKNLRYNKNAPFHVMVTSYQMVVTDANYLQKMKWQYMILDEAQAIKSSQSSRWKNLLSFHCRNRLLLTGTPIQNSMQELWALLHFIMPSLFDSHDEFNEWFSKDIESHAEANTKLNQQQLRRLHMILKPFMLRRVKKNVQSELGDKIEIDVLCDLTQRQAKLYQVLKSQISTNYDAIENAATNDSTSNSASNSGSDQNLINAVMQFRKVCNHPDLFERADVDSPFSFTTFGKTTSMLTASVANNNSSVISNSNMNLSSMSSNNISNGKFTDLIYSSRNPIKYSLPRLIYEDLILPNYNNDVDIANKLKNVKFNIFNPSTNYELCLFLSKLTGEPSLNEFFRVSTTPLLKRVIERTNGPKNTDSLSFKTITQELLEVTRNAPSEGVMASLLNVEKHAYEREYLNCIQRGYHPNVSAPPVTIEVLGSSHVTNSINNELFDPLISQALSDIPAITQYNMHVKKGIPVEDFPKTGLFPEPLNKNFSSNISMPSMDRFITESAKLRKLDELLVKLKSEGHRVLIYFQMTKMMDLMEEYLTYRQYNHIRLDGSSKLEDRRDLVHDWQTNPEIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTIDSQAMDRAHRLGQTRQVTVYRLLVRGTIEERMRDRAKQKEQVQQVVMEGKTQEKNIKTIEVGENDSEVTREGSKSISQDGIKEAASALA

Entity 2 Entity 2 polymer

Description description	Actin-related protein 5
Molecular weight formula_weight	87682.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MSSRDASLTPLKAVVIDDPPLRQTPEPFDEQSAYNPQSPIAIDFGSSKLRAGFVNHATPTHIFPNALTKFRDRKLNKNFTFVGNDTLLDQAVRSQSRSPFDGPFVTNWNLTEEILDYTFHHLGVVPDNGIPNPILLTERLATVQSQRTNWYQILFETYNVPGVTFGIDSLFSFYNYNPSGNKTGLVISCGHEDTNVIPVVDGAGILTDAKRINWGGHQAVDYLNDLMALKYPYFPTKMSYLQYETMYKDYCYVSRNYDEDIEKILTLENLDTNDVVVEAPFTEVLQPQKTEEELRIQAEKRKETGKRLQEQARLKRMEKLVQKQEEFEYFSKVRDQLIDEPKKKVLSVLQNAGFDDERDFKKYLHSLEQSLKKAQMVEAEDDSHLDEMNEDKTAQKFDLLDIADEDLNEDQIKEKRKQRFLKASQDARQKAKEEKERVAKEEEEKKLKEQQWRETDLNGWIKDKRLKLNKLIKRRKEKLKLRDEMKDRKSQVSQNRMKNLASLAEDNVKQGAKRNRHQATIDNDPNDTFGANDEDWLIYTDITQNPEAFEEALEYEYKDIVELERLLLEHDPNFTEEDTLEAQYDWRNSILHLFLRGPRPHDSENIHEQHQMHLNVERIRVPEVIFQPTMGGQDQAGICELSETILLKKFGSQPGKLSQTSIDMVNNVLITGGNAKVPGLKERIVKEFTGFLPTGTNITVNMSSDPSLDAWKGMAALARNEEQYRKTVISKKEYEEYGPEYIKEHKLGNTKYFED

Entity 3 Entity 3 polymer

Description description	Chromatin-remodeling complex subunit IES6
Molecular weight formula_weight	18565.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRHKSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTGLKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK

Entity 4 Entity 4 polymer

Description description	RuvB-like protein 1
Molecular weight formula_weight	50516.9 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T,V,X

MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGVIVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTETLMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLRLDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKKKEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGVAELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVPPDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLAPCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYL

Entity 5 Entity 5 polymer

Description description	RuvB-like protein 2
Molecular weight formula_weight	50539.4 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,W,Y

MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKMVQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQAFRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLTKEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVSLHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYNEQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEVEDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK

Entity 6 Entity 6 polymer

Description description	Ino eighty subunit 2
Molecular weight formula_weight	36211.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MDSEASDIEAELSDSVSAGGEEYIDDDDYTEDIDDQIVTAKSSRRTARRSVPKGVRTSKRIRDKELSVEVDEDYDEEEDVLSPSKKRHLHTRSMDKRQVAATASEKSDIGDSKGNDGEIEDGILEEEESLEKELNRGGGKEVEKSEESYYAQNDVGQKGEEEQDGESGGYEDNEPSISKESDELVSVVNGNGNEEDDEVEATKENTTDSTRSTTTRSKMLLDLLEDGGSKKKLTDEEIQLRRAENARKRKNLSEKRLEEEKQDTINKLLKKRAGKSRSHLPNDDEKNDGSSSFVKPRRPYNSEGMTRILRRYEEDLFCTF

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

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Resolution resolution	3.01 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	40107

DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module

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

Chromatin-remodeling ATPase INO80

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin-related protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromatin-remodeling complex subunit IES6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RuvB-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RuvB-like protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ino eighty subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9ccd__assembly_1__model_1

9ccd__assembly_1__model_1 | I(q)

9ccd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)