SAXSdb — 9q80

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1. Structure Basics

entry_id	9q80
deposition_date	2025-02-21
title	Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome
keywords	DNA-binding protein, NHEJ, Ku70/80, nucleosome, DNA BINDING PROTEIN; 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	62.12 Å
rg_electron	64.19 Å
i0	2979110000.00
molecular_weight	399530.0 kDa
excluded_volume	475460 Å³
envelope_volume	786430 Å³
shell_volume	107060 Å³
envelope_diameter	216.0 Å
shell_rg	60.47 Å
envelope_rg	61.71 Å
shape_rg	64.30 Å
total_rg	63.80 Å
total_atoms	27768
n_residues	3176
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	226.7 Å
rg_real	62.42 Å
rg_real_error	2.48 Å
i0_real	2.9790e+09
i0_real_error	6.8240e+07
rg_reciprocal	61.85 Å
i0_reciprocal	2976000000.0000
total_estimate	0.8487
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	63.5 Å
skewness	0.417
kurtosis	-0.330
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0032
highest_alpha	193700000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.759

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	X-ray repair cross-complementing protein 6
formula_weight	69945.0 kDa
ec_number	3.6.4.-,4.2.99.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,M
atom_count	27768

MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	X-ray repair cross-complementing protein 5
formula_weight	82812.4 kDa
ec_number	3.6.4.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,N

MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFEEGGDVDDLLDMI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Histone H2AX
formula_weight	15172.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

MSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGHYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTSATVGPKAPSGGKKATQASQEY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B type 1-J
formula_weight	13935.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	Histone H3.1
formula_weight	15437.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,A

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,B

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 7 polymer

description	DNA
formula_weight	46998.9 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGAT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 8 polymer

description	DNA
formula_weight	47457.2 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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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	3.390 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.39 Å
resolution_method	—
num_particles	16914

fit	/app/data/saxs_computation/q8/9q80/9q80.fit
pddf	/app/data/pr_computation/q8/9q80/9q80.pr.out
profile	/app/data/saxs_computation/q8/9q80/9q80.dat

Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)