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9xzr

Trm10-tRNA complex (open conformation)

Method: ELECTRON MICROSCOPY D_max: 85.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xzr
deposition_date	2025-08-27
title	Trm10-tRNA complex (open conformation)
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	24.49 Å
rg_electron	23.44 Å
i0	60409600.00
molecular_weight	43834.0 kDa
excluded_volume	47564 Å³
envelope_volume	66156 Å³
shell_volume	24437 Å³
envelope_diameter	89.3 Å
shell_rg	29.40 Å
envelope_rg	23.23 Å
shape_rg	23.37 Å
total_rg	24.10 Å
total_atoms	2981
n_residues	247
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	85.0 Å
rg_real	24.47 Å
rg_real_error	0.61 Å
i0_real	6.0410e+07
i0_real_error	7.4280e+05
rg_reciprocal	24.48 Å
i0_reciprocal	60410000.0000
total_estimate	0.8725
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.317
kurtosis	-0.286
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	4154000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.941

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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	22809.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	2981

GCGCAAGUGGUUUAGUGGUAAAAUCCAACGUUGCCAUCGUUGGGCCCCCGGUUCGAUUCCGGGCUUGCGCA

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	1

Polymer

type	polypeptide(L)
strand_id	B

MSNDEINQNEEKVKRTPPLPPVPEGMSKKQWKKMCKRQRWEENKAKYNAERRVKKKRLRHERSAKIQEYIDRGEEVPQELIREPRINVNQTDSGIEIILDCSFDELMNDKEIVSLSNQVTRAYSANRRANHFAEIKVAPFDKRLKQRFETTLKNTNYENWNHFKFLPDDKIMFGDEHISKDKIVYLTADTEEKLEKLEPGMRYIVGGIVDKNRYKELCLKKAQKMGIPTRRLPIDEYINLEGRRVLTTTHVVQLMLKYFDDHNWKNAFESVLPPRKLDAEAKSASSSPAPKDT

Source

organism	Saccharomyces cerevisiae BMN1-35
ncbi_taxonomy_id	1216345
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	3.37 Å
resolution_method	—
num_particles	1440392

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

Trm10-tRNA complex (open conformation)

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)