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9vd0

Cryo-EM structure of monomeric Suv3-ssRNA-AMPPNP complex

Method: ELECTRON MICROSCOPY D_max: 102.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vd0
deposition_date	2025-06-07
title	Cryo-EM structure of monomeric Suv3-ssRNA-AMPPNP 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	29.90 Å
rg_electron	29.75 Å
i0	77334000.00
molecular_weight	69709.0 kDa
excluded_volume	87555 Å³
envelope_volume	114440 Å³
shell_volume	33895 Å³
envelope_diameter	106.6 Å
shell_rg	34.70 Å
envelope_rg	29.89 Å
shape_rg	29.78 Å
total_rg	30.13 Å
total_atoms	4898
n_residues	605
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	102.7 Å
rg_real	30.08 Å
rg_real_error	1.05 Å
i0_real	7.7330e+07
i0_real_error	1.2730e+06
rg_reciprocal	30.01 Å
i0_reciprocal	77330000.0000
total_estimate	0.8429
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.9 Å
skewness	0.578
kurtosis	-0.051
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	19280000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.878

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	;RNA (5'-R(PUPU)-3') ;
formula_weight	567.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C
atom_count	4898

Entity 2 polymer

description	ATP-dependent RNA helicase SUPV3L1, mitochondrial
formula_weight	85450.9 kDa
ec_number	3.6.4.13
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MGSSHHHHHHSSGLVPRGSHMASSSASGGSKIPNTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVLDCKDDLRKISDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVRDYKRLTPISVLDHALESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPIRAAGLHPTAEQIEMFAYHLPDATLSNLIDIFVDFSQVDGQYFVCNMDDFKFSAELIQHIPLSLRVRYVFCTAPINKKQPFVCSSLLQFARQYSRNEPLTFAWLRRYIKWPLLPPKNIKDLMDLEAVHDVLDLYLWLSYRFMDMFPDASLIRDLQKELDGIIQDGVHNITKLIKMSETHKLLNLEGFPSGSQSRLSGTLKSQARRTRGTKALGSKATEPPSPDAGELSLASRLVQQGLLTPDMLKQLEKEWMTQQTEHNKEKTESGTHPKGTRRKKKEPDSD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 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	4.420 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.42 Å
resolution_method	—
num_particles	79467

fit	/app/data/saxs_computation/vd/9vd0/9vd0.fit
pddf	/app/data/pr_computation/vd/9vd0/9vd0.pr.out
profile	/app/data/saxs_computation/vd/9vd0/9vd0.dat

Cryo-EM structure of monomeric Suv3-ssRNA-AMPPNP 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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)