5xs0

Structure of a ssDNA bound to the outer DNA binding site of RAD52

Method: X-RAY DIFFRACTION

▼

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

DNA repair protein RAD52 homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 11 DNA 2	;ssDNA (5'-D(CPCPCPCPCPCPCPCPCPC)-3') ; × 1 ;ssDNA (5'-D(CPCPCPCPCPCPCPCP*C)-3') ; × 1	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 11 DNA 2	;ssDNA (5'-D(CPCPCPCPCPC)-3') ; × 1 ;ssDNA (5'-D(CPCPCPCPCPCPCPC)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD52_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–215； UniProt 1–212 Author chain B； PDBConstruct 4–215； UniProt 1–212 Author chain C； PDBConstruct 4–215； UniProt 1–212 Author chain D； PDBConstruct 4–215； UniProt 1–212 Author chain E； PDBConstruct 4–215； UniProt 1–212 Author chain F； PDBConstruct 4–215； UniProt 1–212 Author chain G； PDBConstruct 4–215； UniProt 1–212 Author chain H； PDBConstruct 4–215； UniProt 1–212 Author chain I； PDBConstruct 4–215； UniProt 1–212 Author chain J； PDBConstruct 4–215； UniProt 1–212 Author chain K； PDBConstruct 4–215； UniProt 1–212 Author chain L； PDBConstruct 4–215； UniProt 1–212 Author chain M； PDBConstruct 4–215； UniProt 1–212 Author chain N； PDBConstruct 4–215； UniProt 1–212 Author chain O； PDBConstruct 4–215； UniProt 1–212 Author chain P； PDBConstruct 4–215； UniProt 1–212 Author chain Q； PDBConstruct 4–215； UniProt 1–212 Author chain R； PDBConstruct 4–215； UniProt 1–212 Author chain S； PDBConstruct 4–215； UniProt 1–212 Author chain T； PDBConstruct 4–215； UniProt 1–212 Author chain U； PDBConstruct 4–215； UniProt 1–212 Author chain V； PDBConstruct 4–215； UniProt 1–212

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5xs0
Deposition date deposition_date	2017-06-11
Structure title title	Structure of a ssDNA bound to the outer DNA binding site of RAD52
Keywords keywords	Protein-DNA complex, ssDNA annealing protein, DNA repair protein, RECOMBINATION; RECOMBINATION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5xs0__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5xs0__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xs0__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	40.88 Å
Rg (electron density)	40.28 Å
Total Rg	40.93 Å
Atom count	16175
Residues	2032
Excluded volume	285190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xs0__assembly_1__model_1`	tridecameric （13）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5xs0__assembly_2__model_1`	tridecameric （13）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA repair protein RAD52 homolog
Molecular weight formula_weight	23713.8 kDa
Source method src_method	man
Copy count entity_count	22

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
Atom count atom_count	32445

GSHMSGTEEAILGGRDSHPAAGGGSVLCFGQCQYTAEEYQAIQKALRQRLGPEYISSRMAGGGQKVCYIEGHRVINLANEMFGYNGWAHSITQQNVDFVDLNNGKFYVGVCAFVRVQLKDGSYHEDVGYGVSEGLKSKALSLEKARKEAVTDGLKRALRSFGNALGNCILDKDYLRSLNKLPRQLPLEVDLTKAKRQDLEPSVEEARYNSCRPNM

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;ssDNA (5'-D(CPCPCPCPCPC)-3') ;
Molecular weight formula_weight	1690.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	W

CCCCCC

Entity 3 Entity 3 polymer

Description description	;ssDNA (5'-D(CPCPCPCPCPCPCPC)-3') ;
Molecular weight formula_weight	2268.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X

CCCCCCCC

Entity 4 Entity 4 polymer

Description description	;ssDNA (5'-D(CPCPCPCPCPCPCPCPCPC)-3') ;
Molecular weight formula_weight	2846.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

CCCCCCCCCC

Entity 5 Entity 5 polymer

Description description	;ssDNA (5'-D(CPCPCPCPCPCPCPCP*C)-3') ;
Molecular weight formula_weight	2557.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Z

CCCCCCCCC

▼

6. Fold Classification (SCOP + CATH) 22 domains

CATH v4.4 (22 domains)

Domain ID domain_id	5xs0A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0G01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0H01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0I01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0J01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0K01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0L01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0M01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0N01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0O01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0P01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0Q01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0R01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0S01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0T01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0U01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

Domain ID domain_id	5xs0V01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	80 — DNA repair protein Rad52/59/22

▶

Unit-cell length a length_a	100.224 Å
Unit-cell length b length_b	164.408 Å
Unit-cell length c length_c	166.087 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	44

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.529 Å
R factor r_factor	0.2225
R_work r_work	0.2210
R_free r_free	0.2506

Structure of a ssDNA bound to the outer DNA binding site of RAD52

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

DNA repair protein RAD52 homolog

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

5xs0__assembly_2__model_1

5xs0__assembly_2__model_1 | I(q)

5xs0__assembly_2__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 22 domains

CATH v4.4 (22 domains)

7. Citations (1)

Structure of a ssDNA bound to the outer DNA binding site of RAD52

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

DNA repair protein RAD52 homolog

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

5xs0__assembly_2__model_1

5xs0__assembly_2__model_1 | I(q)

5xs0__assembly_2__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 22 domains

CATH v4.4 (22 domains)

7. Citations (1)