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9q23

DX2-CX3-RAD51 structure in the intermediate state

Method: ELECTRON MICROSCOPY D_max: 138.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q23
deposition_date	2025-08-14
title	DX2-CX3-RAD51 structure in the intermediate state
keywords	RAD51 paralog, DX2-CX3 complex, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	43.30 Å
rg_electron	43.06 Å
i0	609645000.00
molecular_weight	201490.0 kDa
excluded_volume	251800 Å³
envelope_volume	333790 Å³
shell_volume	63714 Å³
envelope_diameter	145.8 Å
shell_rg	48.65 Å
envelope_rg	42.63 Å
shape_rg	43.06 Å
total_rg	43.30 Å
total_atoms	23659
n_residues	1797
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	138.4 Å
rg_real	43.28 Å
rg_real_error	1.35 Å
i0_real	6.0960e+08
i0_real_error	1.2020e+07
rg_reciprocal	43.30 Å
i0_reciprocal	609700000.0000
total_estimate	0.8316
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.1 Å
skewness	0.225
kurtosis	-0.701
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	100400000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 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
atom_count	23659

MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKTQLCMQLAVDVQIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLQLIAEKHKGEEHRKALEDFTLDNILSHIYYFRCRDYTELLAQVYLLPDFLSEHSKVRLVIVDGIAFPFRHDLDDLSLRTRLLNGLAQQMISLANNHRLAVILTNQMTTKIDRNQALLVPALGESWGHAATIRLIFHWDRKQRLATLYKSPSQKECTVLFQIKPQGFRDTVVTSACSLQTEGSLSTRKRSRDPEEEL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 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	D

MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNVLYVDSNGGLTASRLLQLLQAKTQDEEEQAEALRRIQVVHAFDIFQMLDVLQELRGTVAQQVTGSSGTVKVVVVDSVTAVVSPLLGGQQREGLALMMQLARELKTLARDLGMAVVVTNHITRDRDSGRLKPALGRSWSFVPSTRILLDTIEGAGASGGRRMACLAKSSRQPTGFQEMVDIGTWGTSEQSATLQGDQT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	DNA repair protein RAD51 homolog 1
formula_weight	37009.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,I

MAMQMQLEANADTSVEEESFGPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDAKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 polymer

description	ssDNA (6-mer)
formula_weight	1780.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	H

TTTTTT

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	R

MDLDLLDLNPRIIAAIKKAKLKSVKEVLHFSGPDLKRLTNLSSPEVWHLLRTASLHLRGSSILTALQLHQQKERFPTQHQRLSLGCPVLDALLRGGLPLDGITELAGRSSAGKTQLALQLCLAVQFPRQHGGLEAGAVYICTEDAFPHKRLQQLMAQQPRLRTDVPGELLQKLRFGSQIFIEHVADVDTLLECVNKKVPVLLSRGMARLVVIDSVAAPFRCEFDSQASAPRARHLQSLGATLRELSSAFQSPVLCINQVTEAMEEQGAAHGPLGFWDERVSPALGITWANQLLVRLLADRLREEEAALGCPARTLRVLSAPHLPPSSCSYTISAEGVRGTPGTQSH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

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	X

MCSAFHRAESGTELLARLEGRSSLKEIEPNLFADEDSPVHGDILEFHGPEGTGKTEMLYHLTARCILPKSEGGLEVEVLFIDTDYHFDMLRLVTILEHRLSQSSEEIIKYCLGRFFLVYCSSSTHLLLTLYSLESMFCSHPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLRKCSQCLEKLVNDYRLVLFATTQTIMQKASSSSEEPSHASRRLCDVDIDYRPYLCKAWQQLVKHRMFFSKQDDSQSSNQFSLVSRCLKSNSLKKHFFIIGESGVEFC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 7 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 9 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

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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	2.84 Å
resolution_method	—
num_particles	55384

fit	/app/data/saxs_computation/q2/9q23/9q23.fit
pddf	/app/data/pr_computation/q2/9q23/9q23.pr.out
profile	/app/data/saxs_computation/q2/9q23/9q23.dat

DX2-CX3-RAD51 structure in the intermediate state

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

EM 3D

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)