SAXSdb — 9e6l

▼

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

DNA repair and recombination protein RAD54

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 1	;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3') ; × 1 DNA repair protein RAD51 × 6 （P25454） ADENOSINE-5'-TRIPHOSPHATE × 6 MAGNESIUM ION × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD54_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–34； UniProt 103–136 Author chain H； PDBConstruct 1–34； UniProt 103–136 Author chain I； PDBConstruct 1–34； UniProt 103–136 Author chain J； PDBConstruct 1–34； UniProt 103–136 Author chain K； PDBConstruct 1–34； UniProt 103–136

DNA repair protein RAD51

Saccharomyces cerevisiae

UniProt P25454

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 1	DNA repair and recombination protein RAD54 × 5 （P32863） ;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3') ; × 1 ADENOSINE-5'-TRIPHOSPHATE × 6 MAGNESIUM ION × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD51_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–321； UniProt 80–400 Author chain B； PDBConstruct 1–321； UniProt 80–400 Author chain C； PDBConstruct 1–321； UniProt 80–400 Author chain D； PDBConstruct 1–321； UniProt 80–400 Author chain E； PDBConstruct 1–321； UniProt 80–400 Author chain F； PDBConstruct 1–321； UniProt 80–400

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	9e6l
Deposition date deposition_date	2024-10-30
Structure title title	Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Keywords keywords	Rad51, DNA recombinase, Homologous recombination, DNA repair, RECOMBINATION, RECOMBINATION-DNA complex; RECOMBINATION/DNA
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9e6l__assembly_1__model_1

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

Download this curve (.dat)

9e6l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9e6l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.58 Å
Rg (electron density)	45.66 Å
Total Rg	45.80 Å
Atom count	16587
Residues	2112
Excluded volume	293930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9e6l__assembly_1__model_1`	12-meric （12）	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 and recombination protein RAD54
Molecular weight formula_weight	4033.7 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	syn
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K
Atom count atom_count	16587

RRKDALSAQRLAKDPTRLSHIQYTLRRSFTVPIK

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3') ;
Molecular weight formula_weight	5430.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X

TTTTTTTTTTTTTTTTTT

Entity 3 Entity 3 polymer

Description description	DNA repair protein RAD51
Molecular weight formula_weight	34930.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,B,E,A,D

FVPIEKLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARLVPMGFVTAADFHMRRSELICLTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVSIAQRFGLDPDDALNNVAYARAYNADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRGELSARQMHLAKFMRALQRLADQFGVAVVVTNQVVAQVDGGMAFNPDPKKPIGGNIMAHSSTTRLGFKKGKGCQRLCKVVDSPCLPEAECVFAIYEDGVGDPREEDE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer'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	6

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

▶

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	3.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	363379

Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide

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

DNA repair and recombination protein RAD54

State in the Current Structure

Other States of the Same Protein in the Database

DNA repair protein RAD51

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

9e6l__assembly_1__model_1

9e6l__assembly_1__model_1 | I(q)

9e6l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide

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

DNA repair and recombination protein RAD54

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA repair protein RAD51

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

9e6l__assembly_1__model_1

9e6l__assembly_1__model_1 | I(q)

9e6l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)