SAXSdb — 4yir

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

DNA repair protein RAD4

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–DNA	Heteromer	Protein 2 DNA 2	UV excision repair protein RAD23 × 1 （P32628） ;DNA (5'-D(TPTPGPAPCPTPCP(G47)PAPCPAPTPCPCPCPCPCPGPCPTPAPCPAPA)-3') ; × 1 ;DNA (5'-D(APTPTPGPTPAPGPCPGGPGPGPAPTPGPTPCPGPAPGPTPCP*A)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–538； UniProt 101–632

UV excision repair protein RAD23

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32628

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	DNA repair protein RAD4 × 1 （P14736） ;DNA (5'-D(TPTPGPAPCPTPCP(G47)PAPCPAPTPCPCPCPCPCPGPCPTPAPCPAPA)-3') ; × 1 ;DNA (5'-D(APTPTPGPTPAPGPCPGGPGPGPAPTPGPTPCPGPAPGPTPCP*A)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD23_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 3–171； UniProt 230–398

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	4yir
Deposition date deposition_date	2015-03-02
Structure title title	Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA
Keywords keywords	;DNA damage repair, nucleotide excision repair, protein-DNA interactions, protein-DNA crosslinking, protein-DNA complex, xeroderma pigmentosum, beta-hairpin, transglutaminase domain, disulfide crosslinking, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/DNA
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.

4yir__assembly_1__model_1

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

Download this curve (.dat)

4yir__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yir__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.75 Å
Rg (electron density)	31.10 Å
Total Rg	31.70 Å
Atom count	10590
Residues	598
Excluded volume	94800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yir__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA repair protein RAD4
Molecular weight formula_weight	62588.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10590

GSSRAMGNEVAGVEDISVEITPSSKRNSDARRTSRNCSSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLHPQKDEELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDISVQGFVAMLRACNVNARLIMSCQPPDFTNMKIDTSLNGNNAYKDMVKYPIFWCEVWDKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDYEDQYFFRRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKGEAEEEDERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIEFI

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	UV excision repair protein RAD23
Molecular weight formula_weight	17783.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

GSGNASSGALGTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEAVGDNMQDVMEGADDMVEGEDIEVTGEAAAAGLGQGEGEGSFQVDYTPEDDQAISRLCELGFERDLVIQVYFACDKNEEAAANILFSDHAD

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	;DNA (5'-D(TPTPGPAPCPTPCP(G47)PAPCPAPTPCPCPCPCPCPGPCPTPAPCPAPA)-3') ;
Molecular weight formula_weight	7294.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	W

TTGACTCGACATCCCCCGCTACAA

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	synthetic construct

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(APTPTPGPTPAPGPCPGGPGPGPAPTPGPTPCPGPAPGPTPCP*A)-3') ;
Molecular weight formula_weight	7505.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

ATTGTAGCGGGGGATGTCGAGTCA

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	synthetic construct

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4yirA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	260 — Coagulation Factor XIII; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Transglutaminase-like

Domain ID domain_id	4yirA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	20 — Anthopleurin-A
Homologous superfamily homologous superfamily	110 — Rad4, beta-hairpin domain BHD1

Domain ID domain_id	4yirA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	290 — Rad4, beta-hairpin domain BHD2

Domain ID domain_id	4yirX00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	540 — XPC-binding domain

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Unit-cell length a length_a	79.405 Å
Unit-cell length b length_b	79.405 Å
Unit-cell length c length_c	404.366 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	39.700 Å
R factor r_factor	0.1970
R_work r_work	0.1923
R_free r_free	0.2529

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA

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

DNA repair protein RAD4

State in the Current Structure

Other States of the Same Protein in the Database

UV excision repair protein RAD23

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

4yir__assembly_1__model_1

4yir__assembly_1__model_1 | I(q)

4yir__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 (4)

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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA

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

DNA repair protein RAD4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UV excision repair protein RAD23

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

4yir__assembly_1__model_1

4yir__assembly_1__model_1 | I(q)

4yir__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 (4)

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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)