9zzr

Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex

Method: ELECTRON MICROSCOPY

▼

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

DNA repair protein RAD51 homolog 1

Homo sapiens

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(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') ; × 1 DNA repair protein XRCC2 × 1 （O43543） DNA repair protein RAD51 homolog 4 × 1 （O75771） DNA repair protein RAD51 homolog 3 × 1 （O43502） DNA repair protein XRCC3 × 1 （O43542） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 11	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAD51_HUMAN
Isoform	—
PDB entities	1, 2, 8
Chains and sequence ranges	Author chain R； PDBConstruct 1–316； UniProt 22–337 Author chain V； PDBConstruct 1–316； UniProt 22–337 Author chain E； PDBConstruct 1–317； UniProt 22–338 Author chain K； PDBConstruct 1–317； UniProt 22–338 Author chain O； PDBConstruct 1–317； UniProt 22–338 Author chain W； PDBConstruct 1–317； UniProt 22–338 Author chain F； PDBConstruct 1–314； UniProt 24–337

DNA repair protein XRCC2

Homo sapiens

UniProt O43543

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 protein RAD51 homolog 1 × 2 （Q06609） DNA repair protein RAD51 homolog 1 × 4 （Q06609） ;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') ; × 1 DNA repair protein RAD51 homolog 4 × 1 （O75771） DNA repair protein RAD51 homolog 3 × 1 （O43502） DNA repair protein XRCC3 × 1 （O43542） DNA repair protein RAD51 homolog 1 × 1 （Q06609） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 11	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain X； PDBConstruct 1–260； UniProt 21–280

DNA repair protein RAD51 homolog 4

Homo sapiens

UniProt O75771

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 protein RAD51 homolog 1 × 2 （Q06609） DNA repair protein RAD51 homolog 1 × 4 （Q06609） ;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') ; × 1 DNA repair protein XRCC2 × 1 （O43543） DNA repair protein RAD51 homolog 3 × 1 （O43502） DNA repair protein XRCC3 × 1 （O43542） DNA repair protein RAD51 homolog 1 × 1 （Q06609） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 11	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RA51D_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain D； PDBConstruct 1–313； UniProt 2–314

DNA repair protein RAD51 homolog 3

Homo sapiens

UniProt O43502

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 protein RAD51 homolog 1 × 2 （Q06609） DNA repair protein RAD51 homolog 1 × 4 （Q06609） ;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') ; × 1 DNA repair protein XRCC2 × 1 （O43543） DNA repair protein RAD51 homolog 4 × 1 （O75771） DNA repair protein XRCC3 × 1 （O43542） DNA repair protein RAD51 homolog 1 × 1 （Q06609） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 11	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RA51C_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–339； UniProt 10–348

DNA repair protein XRCC3

Homo sapiens

UniProt O43542

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 protein RAD51 homolog 1 × 2 （Q06609） DNA repair protein RAD51 homolog 1 × 4 （Q06609） ;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') ; × 1 DNA repair protein XRCC2 × 1 （O43543） DNA repair protein RAD51 homolog 4 × 1 （O75771） DNA repair protein RAD51 homolog 3 × 1 （O43502） DNA repair protein RAD51 homolog 1 × 1 （Q06609） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 11	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC3_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain B； PDBConstruct 1–346； UniProt 1–346

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	9zzr
Deposition date deposition_date	2026-01-07
Structure title title	Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
Keywords keywords	Pentameric, RAD51, XRCC3, RAD51C, RAD51D, XRCC2, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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.

9zzr__assembly_1__model_1

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

Download this curve (.dat)

9zzr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9zzr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.81 Å
Rg (electron density)	60.64 Å
Total Rg	60.57 Å
Atom count	26730
Residues	3390
Excluded volume	474530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9zzr__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	DNA repair protein RAD51 homolog 1
Molecular weight formula_weight	34464.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,V
Atom count atom_count	26730

PQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDA

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	DNA repair protein RAD51 homolog 1
Molecular weight formula_weight	34593.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,O,E,K

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 3 Entity 3 polymer

Description description	;DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') ;
Molecular weight formula_weight	6951.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TTTTTTTTTTTTTTTTTTTTTTT

Entity 4 Entity 4 polymer

Description description	DNA repair protein XRCC2
Molecular weight formula_weight	29832.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

RSSLKEIEPNLFADEDSPVHGDILEFHGPEGTGKTEMLYHLTARCILPKSEGGLEVEVLFIDTDYHFDMLRLVTILEHRLSQSSEEIIKYCLGRFFLVYCSSSTHLLLTLYSLESMFCSHPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLRKCSQCLEKLVNDYRLVLFATTQTIMQKASSSSEEPSHASRRLCDVDIDYRPYLCKAWQQLVKHRMFFSKQDDSQSSNQFSLVSRCLKSNSLKKHFFIIGESGVEFC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	DNA repair protein RAD51 homolog 4
Molecular weight formula_weight	33548.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNVLYVDSNGGLTASRLLQLLQAKTQDEEEQAEALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQQREGLALMMQLARELKTLARDLGMAVVVTNHITRDRDSGRLKPALGRSWSFVPSTRILLDTIEGAGASGGRRMACLAKSSRQPTGFQEMVDIGTW

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	DNA repair protein RAD51 homolog 3
Molecular weight formula_weight	38021.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKTQLCMQLAVDVQIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLQLIAEKHKGEEHRKALEDFTLDNILSHIYYFRCRDYTELLAQVYLLPDFLSEHSKVRLVIVDGIAFPFRHDLDDLSLRTRLLNGLAQQMISLANNHRLAVILTNQMTTKIDRNQALLVPALGESWGHAATIRLIFHWDRKQRLATLYKSPSQKECTVLFQIKPQGFRD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 7 Entity 7 polymer

Description description	DNA repair protein XRCC3
Molecular weight formula_weight	37899.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDLDLLDLNPRIIAAIKKAKLKSVKEVLHFSGPDLKRLTNLSSPEVWHLLRTASLHLRGSSILTALQLHQQKERFPTQHQRLSLGCPVLDALLRGGLPLDGITELAGRSSAGKTQLALQLCLAVQFPRQHGGLEAGAVYICTEDAFPHKRLQQLMAQQPRLRTDVPGELLQKLRFGSQIFIEHVADVDTLLECVNKKVPVLLSRGMARLVVIDSVAAPFRCEFDSQASAPRARHLQSLGATLRELSSAFQSPVLCINQVTEAMEEQGAAHGPLGFWDERVSPALGITWANQLLVRLLADRLREEEAALGCPARTLRVLSAPHLPPSSCSYTISAEGVRGTPGTQSH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 8 Entity 8 polymer

Description description	DNA repair protein RAD51 homolog 1
Molecular weight formula_weight	34239.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

PISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDA

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 9 Entity 9 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	11

▶

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	2.95 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	123502

Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex

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

DNA repair protein RAD51 homolog 1

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 XRCC2

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 homolog 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

DNA repair protein RAD51 homolog 3

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 XRCC3

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

9zzr__assembly_1__model_1

9zzr__assembly_1__model_1 | I(q)

9zzr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 non-polymer

7. Citations (1)