SAXSdb — 8a5o

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

Chromatin-remodeling ATPase INO80

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Actin-like protein ARP8 × 1 （Q12386） Actin × 1 （P60010） Actin-related protein 4 × 1 （P80428） Ino eighty subunit 4 × 1 （Q08561） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	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 G； PDBConstruct 1–598； UniProt 1–598

Actin-like protein ARP8

Saccharomyces cerevisiae S288C

UniProt Q12386

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin × 1 （P60010） Actin-related protein 4 × 1 （P80428） Ino eighty subunit 4 × 1 （Q08561） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP8_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–881； UniProt 1–881

Actin

Saccharomyces cerevisiae S288C

UniProt P60010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-like protein ARP8 × 1 （Q12386） Actin-related protein 4 × 1 （P80428） Ino eighty subunit 4 × 1 （Q08561） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACT_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain V； PDBConstruct 1–375； UniProt 1–375

Actin-related protein 4

Saccharomyces cerevisiae S288C

UniProt P80428

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-like protein ARP8 × 1 （Q12386） Actin × 1 （P60010） Ino eighty subunit 4 × 1 （Q08561） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP4_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain W； PDBConstruct 1–489； UniProt 1–489

Ino eighty subunit 4

Saccharomyces cerevisiae S288C

UniProt Q08561

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Chromatin-remodeling ATPase INO80 × 1 （P53115） Actin-like protein ARP8 × 1 （Q12386） Actin × 1 （P60010） Actin-related protein 4 × 1 （P80428） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IES4_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain X； PDBConstruct 1–116； UniProt 1–116

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	8a5o
Deposition date deposition_date	2022-06-15
Structure title title	Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80
Keywords keywords	chromatin remodeler, INO80, Actin-related protein, 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.

8a5o__assembly_1__model_1

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

Download this curve (.dat)

8a5o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8a5o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.98 Å
Rg (electron density)	40.70 Å
Total Rg	40.97 Å
Atom count	12571
Residues	1555
Excluded volume	223640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8a5o__assembly_1__model_1`	pentameric （5）	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	72170.6 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	12571

MSLAVLLNKEDKDISDFSKTTAGKSAKKNSRERVADVAPTRVLDKKQAYLSQLNSEFNRIKRRDSIEQLYQDWKFINLQEFELISEWNQQSKDWQFDNTNDSQDLHFKKLYRDMSMINKEWAEYQSFKNANLSDIINEKDADEDEEDDEDELEDGEEDMEEDEASTGRHTNGKSMRGNGIQKSRKKDAAAAAAIGKAIKDDQTHADTVVTVNGDENEDGNNGEDEDNDNDNENNNDNDNDNENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDFNPDVEKRRKRSSSSSSSTKLSMNSLSLITSKKINKNITINSDRPKIVRELIKMCNKNKHQKIKKRRFTNCIVTDYNPIDSKLNIKITLKQYHVKRLKKLINDAKREREREEALKNNVGLDGNDLDNDEDGSESHKRRKLNNNTANGADDANKRKFNTRHGLPTYGMKMNAKEARAIQRHYDNTYTTIWKDMARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMSNFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKDYKDDDDKGTDYKDDDDK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Actin-like protein ARP8
Molecular weight formula_weight	100322.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MSQEEAESSIIYEEPIDIPLEDDDDEDELEEENSVPLSSQADQENAENESDDSVDNVVGSETPRSVTGLSVDPRDVADEEDEDEEGEDEDEDEDDNDVDNEDENDNDNANENENELGSSRDKRAPPAVQTSKRYKKYPKLDPAKAPPGKKVPLHLLEKRRLGRIKAAEEFAKTLKKIGIEKVETTTLPATGLFQPLMLINQKNYSSDYLKKDDQIFALRDRKFLRNNNTSQISSTNTPDVIDLKSLPHSEASAAPLNDEIDLNDPTATIVIHPGSNSIKIGFPKDDHPVVVPNCVAVPKKWLDLENSEHVENVCLQREQSEEFNNIKSEMEKNFRERMRYYKRKVPGNAHEQVVSFNENSKPEIISEKNDPSPIEWIFDDSKLYYGSDALRCVDEKFVIRKPFRGGSFNVKSPYYKSLAELISDVTKLLEHALNSETLNVKPTKFNQYKVVLVIPDIFKKSHVETFIRVLLTELQFQAVAIIQESLATCYGAGISTSTCVVNIGAAETRIACVDEGTVLEHSAITLDYGGDDITRLFALFLLQSDFPLQDWKIDSKHGWLLAERLKKNFTTFQDADVAVQLYNFMNRSPNQPTEKYEFKLFDEVMLAPLALFFPQIFKLIRTSSHKNSSLEFQLPESRDLFTNELNDWNSLSQFESKEGNLYCDLNDDLKILNRILDAHNIIDQLQDKPENYGNTLKENFAPLEKAIVQSIANASITADVTRMNSFYSNILIVGGSSKIPALDFILTDRINIWRPSLLSSASFPQFYKKLTKEIKDLEGHYVNAPDKTEDENKQILQAQIKEKIVEELEEQHQNIEHQNGNEHIFPVSIIPPPRDMNPALIIWKGASVLAQIKLVEELFITNSDWDVHGSRILQYKCIFTY

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Actin
Molecular weight formula_weight	41735.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQSKRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSYELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYDESGPSIVHHKCF

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Actin-related protein 4
Molecular weight formula_weight	54894.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDIPANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSADTPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGVERLLNDRFR

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	Ino eighty subunit 4
Molecular weight formula_weight	13111.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MSQESSVLSESQEQLANNPKIEDTSPPSANSRDNSKPVLPWDYKNKAIEIKSFSGYKVNFTGWIRRDVREERQRGSEFTASDVKGSDDKATRKKEPADEDPEVKQLEKEGEDGLDS

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8a5oV01
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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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	250000

Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80

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-like protein ARP8

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

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 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ino eighty subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8a5o__assembly_1__model_1

8a5o__assembly_1__model_1 | I(q)

8a5o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)