5nbn

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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	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	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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Actin-related protein 4 × 1 （P80428） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Actin-related protein 4 × 1 （P80428） Actin-like protein ARP8 × 1 （Q12386） Putative DNA helicase INO80 × 1 （P53115） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	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	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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Putative DNA helicase INO80 × 1 （P53115） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Putative DNA helicase INO80 × 1 （P53115） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	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	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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Actin-like protein ARP8 × 1 （Q12386） CALCIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 LATRUNCULIN A × 1	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	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.

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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. 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.

5nbn__assembly_1__model_1

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

Download this curve (.dat)

5nbn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nbn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.74 Å
Rg (electron density)	39.48 Å
Total Rg	39.77 Å
Atom count	11612
Residues	1448
Excluded volume	207060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nbn__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5nbn__assembly_2__model_1`	tetrameric （4）	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	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

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism 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

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism 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

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism 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

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism 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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6. 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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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

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

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-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

Putative DNA helicase 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5nbn__assembly_1__model_1

5nbn__assembly_1__model_1 | I(q)

5nbn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)