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9xzs

Trm10-tRNA complex (Two Trm10 monomers bound to one tRNA)

Method: ELECTRON MICROSCOPY D_max: 104.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xzs
deposition_date	2025-08-27
title	Trm10-tRNA complex (Two Trm10 monomers bound to one tRNA)
keywords	SPOUT methyltransferase, tRNA, methylation, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/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	30.60 Å
rg_electron	31.11 Å
i0	107642000.00
molecular_weight	65569.0 kDa
excluded_volume	74861 Å³
envelope_volume	107650 Å³
shell_volume	30403 Å³
envelope_diameter	110.8 Å
shell_rg	36.31 Å
envelope_rg	30.63 Å
shape_rg	31.10 Å
total_rg	31.52 Å
total_atoms	4513
n_residues	430
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	104.9 Å
rg_real	30.71 Å
rg_real_error	0.90 Å
i0_real	1.0760e+08
i0_real_error	1.6810e+06
rg_reciprocal	30.67 Å
i0_reciprocal	107600000.0000
total_estimate	0.8777
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.3 Å
skewness	0.412
kurtosis	-0.301
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	5896000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Transfer RNA (Gly)
formula_weight	22832.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	4513

GCGCAAGAGGUUUAGUGGUAAAAUCCAACGUUGCCAUCGUUGGGCCCCCGGUUCGAUUCCGGGCUUGCGCA

Entity 2 polymer

description	tRNA (guanine(9)-N1)-methyltransferase
formula_weight	34583.6 kDa
ec_number	2.1.1.221
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C

MSNDEINQNEEKVKRTPPLPPVPEGMSKKQWKKMCKRQRWEENKAKYNAERRVKKKRLRHERSAKIQEYIDRGEEVPQELIREPRINVNQTDSGIEIILDCSFDELMNDKEIVSLSNQVTRAYSANRRANHFAEIKVAPFDKRLKQRFETTLKNTNYENWNHFKFLPDDKIMFGDEHISKDKIVYLTADTEEKLEKLEPGMRYIVGGIVDKNRYKELCLKKAQKMGIPTRRLPIDEYINLEGRRVLTTTHVVQLMLKYFDDHNWKNAFESVLPPRKLDAEAKSASSSPAPKDT

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
formula_weight	395.4 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	3.89 Å
resolution_method	—
num_particles	156897

fit	/app/data/saxs_computation/xz/9xzs/9xzs.fit
pddf	/app/data/pr_computation/xz/9xzs/9xzs.pr.out
profile	/app/data/saxs_computation/xz/9xzs/9xzs.dat

Trm10-tRNA complex (Two Trm10 monomers bound to one tRNA)

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

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)