SAXSdb — 5tgc

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

Actin-related protein 7

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Actin-like protein ARP9 × 1 （Q05123） Regulator of Ty1 transposition protein 102 × 1 （P53330） ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Actin-like protein ARP9 × 1 （Q05123） Regulator of Ty1 transposition protein 102 × 1 （P53330） ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Actin-like protein ARP9 × 2 （Q05123） Regulator of Ty1 transposition protein 102 × 2 （P53330） ADENOSINE-5'-TRIPHOSPHATE × 2 SULFATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP7_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–478； UniProt 1–477 Author chain D； PDBConstruct 2–478； UniProt 1–477

Actin-like protein ARP9

Saccharomyces cerevisiae

UniProt Q05123

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Actin-related protein 7 × 1 （Q12406） Regulator of Ty1 transposition protein 102 × 1 （P53330） ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Actin-related protein 7 × 1 （Q12406） Regulator of Ty1 transposition protein 102 × 1 （P53330） ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Actin-related protein 7 × 2 （Q12406） Regulator of Ty1 transposition protein 102 × 2 （P53330） ADENOSINE-5'-TRIPHOSPHATE × 2 SULFATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARP9_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–467； UniProt 1–467 Author chain E； PDBConstruct 1–467； UniProt 1–467

Regulator of Ty1 transposition protein 102

Saccharomyces cerevisiae

UniProt P53330

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Actin-related protein 7 × 1 （Q12406） Actin-like protein ARP9 × 1 （Q05123） ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Actin-related protein 7 × 1 （Q12406） Actin-like protein ARP9 × 1 （Q05123） ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Actin-related protein 7 × 2 （Q12406） Actin-like protein ARP9 × 2 （Q05123） ADENOSINE-5'-TRIPHOSPHATE × 2 SULFATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RT102_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–158； UniProt 1–157 Author chain F； PDBConstruct 2–158； UniProt 1–157

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	5tgc
Deposition date deposition_date	2016-09-27
Structure title title	Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP
Keywords keywords	Chromatin remodeling complexes, Actin-related protein, ATP-binding site, Nuclear actin, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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.

5tgc__assembly_1__model_1

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

Download this curve (.dat)

5tgc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tgc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.51 Å
Rg (electron density)	31.70 Å
Total Rg	32.28 Å
Atom count	14069
Residues	869
Excluded volume	126420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tgc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5tgc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5tgc__assembly_3__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Actin-related protein 7
Molecular weight formula_weight	55433.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	28278

MMTLNRKCVVIHNGSHRTVAGFSNVELPQCIIPSSYIKRTDEGGEAEFIFGTYNMIDAAAEKRNGDEVYTLVDSQGLPYNWDALEMQWRYLYDTQLKVSPEELPLVITMPATNGKPDMAILERYYELAFDKLNVPVFQIVIEPLAIALSMGKSSAFVIDIGASGCNVTPIIDGIVVKNAVVRSKFGGDFLDFQVHERLAPLIKEENDMENMADEQKRSTDVWYEASTWIQQFKSTMLQVSEKDLFELERYYKEQADIYAKQQEQLKQMDQQLQYTALTGSPNNPLVQKKNFLFKPLNKTLTLDLKECYQFAEYLFKPQLISDKFSPEDGLGPLMAKSVKKAGASINSMKANTSTNPNGLGTSHINTNVGDNNSTASSSNISPEQVYSLLLTNVIITGSTSLIEGMEQRIIKELSIRFPQYKLTTFANQVMMDRKIQGWLGALTMANLPSWSLGKWYSKEDYETLKRDRKQSQATNATNLVPRGSHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Actin-like protein ARP9
Molecular weight formula_weight	53131.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAPFRQDSILIIYPRSQTTLVQFGLNEETFTVPELEIPTQIYRTTRQDGSYTYHSTNKDNKAELIKPIQNGEIIDISAFTQFLRLIFVSILSDRANKNQDAFEAELSNIPLLLITHHSWSQSDLEIITQYVFESLEINNLIQLPASLAATYSMISLQNCCIIDVGTHHTDIIPIVDYAQLDHLVSSIPMGGQSINDSLKKLLPQWDDDQIESLKKSPIFEVLSDDAKKLSSFDFGNENEDEDEGTLNVAEIITSGRDTREVLEERERGQKVKNVKNSDLEFNTFWDEKGNEIKVGKQRFQGCNNLIKNISNRVGLTLDNIDDINKAKAVWENIIIVGGTTSISGFKEALLGQLLKDHLIIEPEEEKSKREEEAKSVLPAATKKKSKFMTNSTAFVPTIEYVQCPTVIKLAKYPDYFPEWKKSGYSEIIFLGAQIVSKQIFTHPKDTFYITREKYNMKGPAALWDVQF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Regulator of Ty1 transposition protein 102
Molecular weight formula_weight	17904.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SMDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRYKTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEALSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	5tgcA01
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	5tgcA02
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	5tgcA03
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	5tgcB01
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	5tgcB02
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	5tgcD01
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	5tgcD02
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	5tgcD03
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	5tgcE01
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	5tgcE02
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

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Unit-cell length a length_a	79.387 Å
Unit-cell length b length_b	87.982 Å
Unit-cell length c length_c	105.430 Å
Unit-cell angle α angle_alpha	109.03 °
Unit-cell angle β angle_beta	104.64 °
Unit-cell angle γ angle_gamma	96.20 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	3.245 Å
Low-resolution limit resolution_low	39.366 Å
R factor r_factor	0.2779
R_work r_work	0.2756
R_free r_free	0.3219

Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP

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

Actin-related protein 7

State in the Current Structure

Other States of the Same Protein in the Database

Actin-like protein ARP9

State in the Current Structure

Other States of the Same Protein in the Database

Regulator of Ty1 transposition protein 102

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5tgc__assembly_1__model_1

5tgc__assembly_1__model_1 | I(q)

5tgc__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 (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP

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

Actin-related protein 7

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 ARP9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Regulator of Ty1 transposition protein 102

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

5tgc__assembly_1__model_1

5tgc__assembly_1__model_1 | I(q)

5tgc__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 (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)