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9svy

XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA

Method: ELECTRON MICROSCOPY D_max: 208.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9svy
deposition_date	2025-10-03
title	XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA
keywords	DNA binding protein, complex, tumor suppresor; DNA BINDING PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	60.26 Å
rg_electron	61.30 Å
i0	2429270000.00
molecular_weight	396680.0 kDa
excluded_volume	489920 Å³
envelope_volume	728010 Å³
shell_volume	102160 Å³
envelope_diameter	236.3 Å
shell_rg	59.99 Å
envelope_rg	60.30 Å
shape_rg	61.32 Å
total_rg	61.20 Å
total_atoms	27704
n_residues	3482
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	208.3 Å
rg_real	60.73 Å
rg_real_error	2.28 Å
i0_real	2.4290e+09
i0_real_error	5.4900e+07
rg_reciprocal	59.83 Å
i0_reciprocal	2426000000.0000
total_estimate	0.8248
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	80.1 Å
skewness	0.546
kurtosis	-0.023
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0002
highest_alpha	409900000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.396

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	DNA repair protein RAD51 homolog 4
formula_weight	35084.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	27704

MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNVLYVDSNGGLTASRLLQLLQAKTQDEEEQAEALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQQREGLALMMQLARELKTLARDLGMAVVVTNHITRDRDSGRLKPALGRSWSFVPSTRILLDTIEGAGASGGRRMACLAKSSRQPTGFQEMVDIGTWGTSEQSATLQGDQT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	dN-31nt
formula_weight	9313.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	M

CCCCCCCCCCTATCGAATCCGTCTAAAGTTA

Entity 3 polymer

description	dN-21nt
formula_weight	6461.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	N

TAACTTTAGACGGATTCGATA

Entity 4 polymer

description	DNA repair protein RAD51 homolog 3
formula_weight	42244.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKTQLCMQLAVDVQIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLQLIAEKHKGEEHRKALEDFTLDNILSHIYYFRCRDYTELLAQVYLLPDFLSEHSKVRLVIVDGIAFPFRHDLDDLSLRTRLLNGLAQQMISLANNHRLAVILTNQMTTKIDRNQALLVPALGESWGHAATIRLIFHWDRKQRLATLYKSPSQKECTVLFQIKPQGFRDTVVTSACSLQTEGSLSTRKRSRDPEEEL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	DNA repair protein XRCC3
formula_weight	37899.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MDLDLLDLNPRIIAAIKKAKLKSVKEVLHFSGPDLKRLTNLSSPEVWHLLRTASLHLRGSSILTALQLHQQKERFPTQHQRLSLGCPVLDALLRGGLPLDGITELAGRSSAGKTQLALQLCLAVQFPRQHGGLEAGAVYICTEDAFPHKRLQQLMAQQPRLRTDVPGELLQKLRFGSQIFIEHVADVDTLLECVNKKVPVLLSRGMARLVVIDSVAAPFRCEFDSQASAPRARHLQSLGATLRELSSAFQSPVLCINQVTEAMEEQGAAHGPLGFWDERVSPALGITWANQLLVRLLADRLREEEAALGCPARTLRVLSAPHLPPSSCSYTISAEGVRGTPGTQSH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 6 polymer

description	DNA repair protein XRCC2
formula_weight	31995.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MCSAFHRAESGTELLARLEGRSSLKEIEPNLFADEDSPVHGDILEFHGPEGTGKTEMLYHLTARCILPKSEGGLEVEVLFIDTDYHFDMLRLVTILEHRLSQSSEEIIKYCLGRFFLVYCSSSTHLLLTLYSLESMFCSHPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLRKCSQCLEKLVNDYRLVLFATTQTIMQKASSSSEEPSHASRRLCDVDIDYRPYLCKAWQQLVKHRMFFSKQDDSQSSNQFSLVSRCLKSNSLKKHFFIIGESGVEFC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 7 polymer

description	DNA repair protein RAD51 homolog 1
formula_weight	37009.1 kDa
src_method	man
entity_count	7

Polymer

type	polypeptide(L)
strand_id	E,F,G,H,I,J,K

MAMQMQLEANADTSVEEESFGPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDAKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 8 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	9

Entity 9 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	10

Entity 10 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	7

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.60 Å
resolution_method	—
num_particles	230120

fit	/app/data/saxs_computation/sv/9svy/9svy.fit
pddf	/app/data/pr_computation/sv/9svy/9svy.pr.out
profile	/app/data/saxs_computation/sv/9svy/9svy.dat

XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)