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9vd1

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

Method: ELECTRON MICROSCOPY D_max: 117.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vd1
deposition_date	2025-06-07
title	Cryo-EM structure of Dimeric 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	36.74 Å
rg_electron	36.02 Å
i0	299195000.00
molecular_weight	141790.0 kDa
excluded_volume	178340 Å³
envelope_volume	230370 Å³
shell_volume	53477 Å³
envelope_diameter	122.2 Å
shell_rg	42.45 Å
envelope_rg	35.26 Å
shape_rg	36.02 Å
total_rg	36.46 Å
total_atoms	9968
n_residues	1239
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	117.4 Å
rg_real	36.63 Å
rg_real_error	0.71 Å
i0_real	2.9920e+08
i0_real_error	5.2140e+06
rg_reciprocal	36.70 Å
i0_reciprocal	299200000.0000
total_estimate	0.8958
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.0 Å
skewness	0.207
kurtosis	-0.539
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	42720000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.841

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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	9968

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	2

Polymer

type	polypeptide(L)
strand_id	B,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	2

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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	4.160 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.16 Å
resolution_method	—
num_particles	93322

fit	/app/data/saxs_computation/vd/9vd1/9vd1.fit
pddf	/app/data/pr_computation/vd/9vd1/9vd1.pr.out
profile	/app/data/saxs_computation/vd/9vd1/9vd1.dat

Cryo-EM structure of Dimeric 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)