← Back to search

9z2r

CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm conformation)

Method: ELECTRON MICROSCOPY D_max: 91.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9z2r
deposition_date	2025-11-05
title	CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm conformation)
keywords	Transferase, Methyltransferase, tRNA, Complex; TRANSFERASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	29.38 Å
rg_electron	28.42 Å
i0	192545000.00
molecular_weight	93241.0 kDa
excluded_volume	109470 Å³
envelope_volume	146660 Å³
shell_volume	41790 Å³
envelope_diameter	95.9 Å
shell_rg	36.85 Å
envelope_rg	28.38 Å
shape_rg	28.42 Å
total_rg	29.12 Å
total_atoms	6449
n_residues	672
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	91.1 Å
rg_real	29.24 Å
rg_real_error	0.50 Å
i0_real	1.9250e+08
i0_real_error	2.6900e+06
rg_reciprocal	29.31 Å
i0_reciprocal	192600000.0000
total_estimate	0.8997
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.1 Å
skewness	0.199
kurtosis	-0.400
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	16710000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.969

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNA cytosine C(5)-methyltransferase NSUN2
formula_weight	88414.7 kDa
ec_number	2.1.1.-,2.1.1.203
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6449

MHHHHHHENLYFQGSGGRRSRGRRLQQQQRPEDAEDGAEGGGKRGEAGWEGGYPEIVKENKLFEHYYQELKIVPEGEWGQFMDALREPLPATLRITGYKSHAKEILHCLKNKYFKELEDLEVDGQKVEVPQPLSWYPEELAWHTNLSRKILRKSPHLEKFHQFLVSETESGNISRQEAVSMIPPLLLNVRPHHKILDMCAAPGSKTTQLIEMLHADMNVPFPEGFVIANDVDNKRCYLLVHQAKRLSSPCIMVVNHDASSIPRLQIDVDGRKEILFYDRILCDVPCSGDGTMRKNIDVWKKWTTLNSLQLHGLQLRIATRGAEQLAEGGRMVYSTCSLNPIEDEAVIASLLEKSEGALELADVSNELPGLKWMPGITQWKVMTKDGQWFTDWDAVPHSRHTQIRPTMFPPKDPEKLQAMHLERCLRILPHHQNTGGFFVAVLVKKSSMPWNKRQPKLQGKSAETRESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSKKDGVCGPPPSKKMKLFGFKEDPFVFIPEDDPLFPPIEKFYALDPSFPRMNLLTRTTEGKKRQLYMVSKELRNVLLNNSEKMKVINTGIKVWCRNNSGEEFDCAFRLAQEGIYTLYPFINSRIITVSMEDVKILLTQENPFFRKLSSETYSQAKDLAKGSIVLKYEPDSANPDALQCPIVLCGWRGKASIRTFVPKNERLHYLRMMGLEVLGEKKKEGVILTNESAASTGQPDNDVTEGQRAGEPNSPDAEEANSPDVTAGCDPAGVHPPR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	tRNA Lys(CTT)
formula_weight	24492.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

GCCCGGCUAGCUCAGUCGGUAGAGCAUGGGACUCUUAAUCCCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCCA

Entity 3 non-polymer

description	SINEFUNGIN
formula_weight	381.4 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	3.710 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.71 Å
resolution_method	—
num_particles	32000

fit	/app/data/saxs_computation/z2/9z2r/9z2r.fit
pddf	/app/data/pr_computation/z2/9z2r/9z2r.pr.out
profile	/app/data/saxs_computation/z2/9z2r/9z2r.dat

CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm 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

Refinement

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)