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9xzm

Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)

Method: ELECTRON MICROSCOPY D_max: 155.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xzm
deposition_date	2025-08-27
title	Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)
keywords	Helicase, Translocase, Fork remodeler, Fork reversal, Replication fork, DNA binding, ISOMERASE-DNA complex; ISOMERASE/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	44.59 Å
rg_electron	41.68 Å
i0	266850000.00
molecular_weight	106750.0 kDa
excluded_volume	122900 Å³
envelope_volume	188260 Å³
shell_volume	43579 Å³
envelope_diameter	163.2 Å
shell_rg	39.37 Å
envelope_rg	43.18 Å
shape_rg	41.47 Å
total_rg	42.08 Å
total_atoms	13586
n_residues	719
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	155.0 Å
rg_real	45.02 Å
rg_real_error	1.93 Å
i0_real	2.6680e+08
i0_real_error	5.1520e+06
rg_reciprocal	44.59 Å
i0_reciprocal	266700000.0000
total_estimate	0.8368
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.3 Å
skewness	0.502
kurtosis	-0.305
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	7379000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.636

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	DNA (45-MER)
formula_weight	13921.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	X
atom_count	13586

GACTGCGAAGGTAGCGACAGATCCCCTGACGAACTGAGTCCTGAG

Entity 2 polymer

description	;DNA (5'-D(TPCPGPCPTPAPCPCPTPTPCPGPCPAPGPTP*C)-3') ;
formula_weight	5114.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

TCGCTACCTTCGCAGTC

Entity 3 polymer

description	DNA (45-MER)
formula_weight	13872.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

CTCAGGACTCAGTTCGTCAGCCCTAGACAGCGATGGAAGCGTCAG

Entity 4 polymer

description	;DNA (5'-D(CPTPGPAPCPGPCPTPTPCPCPAPTPCPGPCPTPGPTPCPTPAP*G)-3') ;
formula_weight	6983.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A

CTGACGCTTCCATCGCTGTCTAG

Entity 5 polymer

description	F-box DNA helicase 1
formula_weight	109518.7 kDa
ec_number	5.6.2.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

SNAMAKSNSVGQDSCQDSEGDMIFPAESSCALPQEGSAGPGSPGSAPPSRKRSWSSEEESNQATGTSRWDGVSKKAPRHHLSVPCTRPREARQEAEDSTSRLSAESGETDQDAGDVGPDPIPDSYYGLLGTLPCQEALSHICSLPSEVLRHVFAFLPVEDLYWNLSLVCHLWREIISDPLFIPWKKLYHRYLMNEEQAVSKVDGILSNCGIEKESDLCVLNLIRYTATTKCSPSVDPERVLWSLRDHPLLPEAEACVRQHLPDLYAAAGGVNIWALVAAVVLLSSSVNDIQRLLFCLRRPSSTVTMPDVTETLYCIAVLLYAMREKGINISNRIHYNIFYCLYLQENSCTQATKVKEEPSVWPGKKTIQLTHEQQLILNHKMEPLQVVKIMAFAGTGKTSTLVKYAEKWSQSRFLYVTFNKSIAKQAERVFPSNVICKTFHSMAYGHIGRKYQSKKKLNLFKLTPFMVNSVLAEGKGGFIRAKLVCKTLENFFASADEELTIDHVPIWCKNSQGQRVMVEQSEKLNGVLEASRLWDNMRKLGECTEEAHQMTHDGYLKLWQLSKPSLASFDAIFVDEAQDCTPAIMNIVLSQPCGKIFVGDPHQQIYTFRGAVNALFTVPHTHVFYLTQSFRFGVEIAYVGATILDVCKRVRKKTLVGGNHQSGIRGDAKGQVALLSRTNANVFDEAVRVTEGEFPSRIHLIGGIKSFGLDRIIDIWILLQPEEERRKQNLVIKDKFIRRWVHKEGFSGFKRYVTAAEDKELEAKIAVVEKYNIRIPELVQRIEKCHIEDLDFAEYILGTVHKAKGLEFDTVHVLDDFVKVPCARHNLPQLPHFRVESFSEDEWNLLYVAVTRAKKRLIMTKSLENILTLAGEYFLQAELTSNVLKTGVVRCCVGQCNNAIPVDTVLTMKKLPITYSNRKENKGGYLCHSCAEQRIGPLAFLTASPEQVRAMERTVENIVLPRHEALLFLVF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 6 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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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	10.27 Å
resolution_method	—
num_particles	7718

fit	/app/data/saxs_computation/xz/9xzm/9xzm.fit
pddf	/app/data/pr_computation/xz/9xzm/9xzm.pr.out
profile	/app/data/saxs_computation/xz/9xzm/9xzm.dat

Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)

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 (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)