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9vcw

Cryo-EM structure of dimeric Suv3-ssRNA complex

Method: ELECTRON MICROSCOPY D_max: 119.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vcw
deposition_date	2025-06-06
title	Cryo-EM structure of dimeric Suv3-ssRNA complex
keywords	Helicase, RNA binding protein, HYDROLASE, HYDROLASE-RNA complex; HYDROLASE/RNA
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	36.56 Å
rg_electron	35.88 Å
i0	293684000.00
molecular_weight	141250.0 kDa
excluded_volume	177990 Å³
envelope_volume	228970 Å³
shell_volume	53284 Å³
envelope_diameter	122.1 Å
shell_rg	42.35 Å
envelope_rg	35.28 Å
shape_rg	35.87 Å
total_rg	36.34 Å
total_atoms	9936
n_residues	1241
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	119.7 Å
rg_real	36.46 Å
rg_real_error	0.86 Å
i0_real	2.9370e+08
i0_real_error	5.3260e+06
rg_reciprocal	36.53 Å
i0_reciprocal	293700000.0000
total_estimate	0.6750
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	41.8 Å
skewness	0.221
kurtosis	-0.511
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	46560000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.996; Smooth: 0.917

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	ATP-dependent RNA helicase SUPV3L1, mitochondrial
formula_weight	85450.9 kDa
ec_number	3.6.4.13
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	9936

MGSSHHHHHHSSGLVPRGSHMASSSASGGSKIPNTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVLDCKDDLRKISDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEMFAYHLPDATLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRYIKWPLLPPKNIKDLMDLEAVHDVLDLYLWLSYRFMDMFPDASLIRDLQKELDGIIQDGVHNITKLIKMSETHKLLNLEGFPSGSQSRLSGTLKSQARRTRGTKALGSKATEPPSPDAGELSLASRLVQQGLLTPDMLKQLEKEWMTQQTEHNKEKTESGTHPKGTRRKKKEPDSD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	;RNA (5'-R(PUPUP*U)-3') ;
formula_weight	873.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

UUU

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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	3.750 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.75 Å
resolution_method	—
num_particles	59709

fit	/app/data/saxs_computation/vc/9vcw/9vcw.fit
pddf	/app/data/pr_computation/vc/9vcw/9vcw.pr.out
profile	/app/data/saxs_computation/vc/9vcw/9vcw.dat

Cryo-EM structure of dimeric Suv3-ssRNA complex

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)