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9vcu

Cryo-EM structure of dimeric Suv3-ADP complex

Method: ELECTRON MICROSCOPY D_max: 117.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vcu
deposition_date	2025-06-06
title	Cryo-EM structure of dimeric Suv3-ADP complex
keywords	dimeric Suv3-ADP complex, HYDROLASE; HYDROLASE
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	36.83 Å
rg_electron	36.09 Å
i0	290744000.00
molecular_weight	140670.0 kDa
excluded_volume	177370 Å³
envelope_volume	232380 Å³
shell_volume	53696 Å³
envelope_diameter	120.1 Å
shell_rg	42.55 Å
envelope_rg	35.40 Å
shape_rg	36.09 Å
total_rg	36.55 Å
total_atoms	9897
n_residues	1237
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	117.1 Å
rg_real	36.71 Å
rg_real_error	0.73 Å
i0_real	2.9070e+08
i0_real_error	4.8830e+06
rg_reciprocal	36.79 Å
i0_reciprocal	290800000.0000
total_estimate	0.8967
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.6 Å
skewness	0.198
kurtosis	-0.534
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	36440000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.842

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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	A,B
atom_count	9897

MGSSHHHHHHSSGLVPRGSHMASSSASGGSKIPNTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVLDCKDDLRKISDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEMFAYHLPDATLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRYIKWPLLPPKNIKDLMDLEAVHDVLDLYLWLSYRFMDMFPDASLIRDLQKELDGIIQDGVHNITKLIKMSETHKLLNLEGFPSGSQSRLSGTLKSQARRTRGTKALGSKATEPPSPDAGELSLASRLVQQGLLTPDMLKQLEKEWMTQQTEHNKEKTESGTHPKGTRRKKKEPDSD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 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	3.840 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.84 Å
resolution_method	—
num_particles	96968

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

Cryo-EM structure of dimeric Suv3-ADP 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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)