← Back to search

9u48

Cryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM

Method: ELECTRON MICROSCOPY D_max: 82.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9u48
deposition_date	2025-03-19
title	Cryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM
keywords	m6A methyltransferase, U6 snRNA, protein-RNA complex, splicing, TRANSFERASE, TRANSFERASE-RNA complex; TRANSFERASE/RNA
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.76 Å
rg_electron	25.62 Å
i0	73132100.00
molecular_weight	54966.0 kDa
excluded_volume	63684 Å³
envelope_volume	84878 Å³
shell_volume	27986 Å³
envelope_diameter	85.3 Å
shell_rg	32.72 Å
envelope_rg	25.57 Å
shape_rg	25.56 Å
total_rg	26.45 Å
total_atoms	3790
n_residues	384
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

▼

3. P(r) Analysis (GNOM)

dmax	82.8 Å
rg_real	26.71 Å
rg_real_error	0.47 Å
i0_real	7.3130e+07
i0_real_error	9.0520e+05
rg_reciprocal	26.73 Å
i0_reciprocal	73130000.0000
total_estimate	0.9106
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	30.9 Å
skewness	0.229
kurtosis	-0.593
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	7715000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.935

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 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
atom_count	3790

MGSSHHHHHHSSGLVPRGSHMASMTDKTDIINFDSLARDYPDLRSFVKNGRIDFWNEDAIRTLGKAILDRDYSLRVEFPENRLCPMVPNRATYIRYIHDLLSSTSGQKDKKRIIGLDIGTGASCIYPLLGCRMYSYDFVGTEIDKFSFETAKSNILQNNMESQIKIVLRSKQDCLLPDTEGMEEFTFVMCNPPFYEHEEDFINFKQNPPSGVCTGVYHEMVTEGGEVGFANKILTESKKRKGIQWYTCMFGKKSSVPAVVDKLREQNISNYGIYELALGKTKRWIICWSFQAMRPHNELIRPSSTSLSKYFPHKVLQNWTLDPELCAQIDDILQKFLDDNKIPWSKKGSVLEISTKSITWSRKARRISKSQTSVSSLEGQMKCELNVIDNQLQCKWIEGYDYNVYESFCSALARALRDNKK

Source

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

Entity 2 polymer

description	U6 small nuclear RNA
formula_weight	31864.0 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

GAUCUUCGGAUCACUUUGGUCAAAUUGAAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCACAAGGAUGACACUGCGACAUUGAGAGAAAACCCAUUUU

Entity 3 non-polymer

description	S-ADENOSYLMETHIONINE
formula_weight	398.4 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

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	2.99 Å
resolution_method	—
num_particles	425927

fit	/app/data/saxs_computation/u4/9u48/9u48.fit
pddf	/app/data/pr_computation/u4/9u48/9u48.pr.out
profile	/app/data/saxs_computation/u4/9u48/9u48.dat

Cryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)