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9u47

Cryo-EM structure of spMETTL16 in complex with U6 snRNA_delta17

Method: ELECTRON MICROSCOPY D_max: 79.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u47
deposition_date	2025-03-19
title	Cryo-EM structure of spMETTL16 in complex with U6 snRNA_delta17
keywords	m6A methyltransferase, U6 snRNA, protein-RNA complex, splicing, TRANSFERASE, TRANSFERASE-RNA complex; TRANSFERASE/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	25.82 Å
rg_electron	24.72 Å
i0	56971000.00
molecular_weight	48908.0 kDa
excluded_volume	57067 Å³
envelope_volume	77427 Å³
shell_volume	26622 Å³
envelope_diameter	81.8 Å
shell_rg	31.35 Å
envelope_rg	24.77 Å
shape_rg	24.64 Å
total_rg	25.58 Å
total_atoms	3374
n_residues	350
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	79.0 Å
rg_real	25.77 Å
rg_real_error	0.47 Å
i0_real	5.6970e+07
i0_real_error	7.6860e+05
rg_reciprocal	25.79 Å
i0_reciprocal	56970000.0000
total_estimate	0.9119
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.221
kurtosis	-0.593
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	6251000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	U6 small nuclear RNA
formula_weight	26476.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B
atom_count	3374

GGUCAAAUUGAAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCACAAGGAUGACACUGCGACAUUGAGAGAAAACCCAUUUU

Entity 2 polymer

description	U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
formula_weight	48442.2 kDa
ec_number	2.1.1.346
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MGSSHHHHHHSSGLVPRGSHMASMTDKTDIINFDSLARDYPDLRSFVKNGRIDFWNEDAIRTLGKAILDRDYSLRVEFPENRLCPMVPNRATYIRYIHDLLSSTSGQKDKKRIIGLDIGTGASCIYPLLGCRMYSYDFVGTEIDKFSFETAKSNILQNNMESQIKIVLRSKQDCLLPDTEGMEEFTFVMCNPPFYEHEEDFINFKQNPPSGVCTGVYHEMVTEGGEVGFANKILTESKKRKGIQWYTCMFGKKSSVPAVVDKLREQNISNYGIYELALGKTKRWIICWSFQAMRPHNELIRPSSTSLSKYFPHKVLQNWTLDPELCAQIDDILQKFLDDNKIPWSKKGSVLEISTKSITWSRKARRISKSQTSVSSLEGQMKCELNVIDNQLQCKWIEGYDYNVYESFCSALARALRDNKK

Source

organism	Schizosaccharomyces pombe
common_name	fission yeast
ncbi_taxonomy_id	4896
host_organism	Escherichia coli BL21(DE3)

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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	3.40 Å
resolution_method	—
num_particles	173139

fit	/app/data/saxs_computation/u4/9u47/9u47.fit
pddf	/app/data/pr_computation/u4/9u47/9u47.pr.out
profile	/app/data/saxs_computation/u4/9u47/9u47.dat

Cryo-EM structure of spMETTL16 in complex with U6 snRNA_delta17

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 (2)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)