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9z3d

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron

Method: ELECTRON MICROSCOPY D_max: 91.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z3d
deposition_date	2025-11-06
title	CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron
keywords	Transferase, Methyltransferase, tRNA, Complex; TRANSFERASE
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	27.33 Å
rg_electron	26.79 Å
i0	191124000.00
molecular_weight	70715.0 kDa
excluded_volume	66949 Å³
envelope_volume	116380 Å³
shell_volume	35598 Å³
envelope_diameter	95.8 Å
shell_rg	34.76 Å
envelope_rg	27.07 Å
shape_rg	26.83 Å
total_rg	27.30 Å
total_atoms	5301
n_residues	613
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	91.6 Å
rg_real	27.27 Å
rg_real_error	0.63 Å
i0_real	1.9110e+08
i0_real_error	2.8820e+06
rg_reciprocal	27.29 Å
i0_reciprocal	191100000.0000
total_estimate	0.8751
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.350
kurtosis	-0.202
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	29940000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.937

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNA cytosine C(5)-methyltransferase NSUN2
formula_weight	88382.6 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	5301

MHHHHHHENLYFQGSGGRRSRGRRLQQQQRPEDAEDGAEGGGKRGEAGWEGGYPEIVKENKLFEHYYQELKIVPEGEWGQFMDALREPLPATLRITGYKSHAKEILHCLKNKYFKELEDLEVDGQKVEVPQPLSWYPEELAWHTNLSRKILRKSPHLEKFHQFLVSETESGNISRQEAVSMIPPLLLNVRPHHKILDMCAAPGSKTTQLIEMLHADMNVPFPEGFVIANDVDNKRCYLLVHQAKRLSSPCIMVVNHDASSIPRLQIDVDGRKEILFYDRILCDVPASGDGTMRKNIDVWKKWTTLNSLQLHGLQLRIATRGAEQLAEGGRMVYSTCSLNPIEDEAVIASLLEKSEGALELADVSNELPGLKWMPGITQWKVMTKDGQWFTDWDAVPHSRHTQIRPTMFPPKDPEKLQAMHLERCLRILPHHQNTGGFFVAVLVKKSSMPWNKRQPKLQGKSAETRESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSKKDGVCGPPPSKKMKLFGFKEDPFVFIPEDDPLFPPIEKFYALDPSFPRMNLLTRTTEGKKRQLYMVSKELRNVLLNNSEKMKVINTGIKVWCRNNSGEEFDCAFRLAQEGIYTLYPFINSRIITVSMEDVKILLTQENPFFRKLSSETYSQAKDLAKGSIVLKYEPDSANPDALQCPIVLCGWRGKASIRTFVPKNERLHYLRMMGLEVLGEKKKEGVILTNESAASTGQPDNDVTEGQRAGEPNSPDAEEANSPDVTAGCDPAGVHPPR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	RNA (26-MER)
formula_weight	9879.9 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

CUCAAGGUAAGCACCUUGCCUGCGGGCUUUC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 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	2.960 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.96 Å
resolution_method	—
num_particles	65000

fit	/app/data/saxs_computation/z3/9z3d/9z3d.fit
pddf	/app/data/pr_computation/z3/9z3d/9z3d.pr.out
profile	/app/data/saxs_computation/z3/9z3d/9z3d.dat

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to a pre-tRNA Leu(CAA) intron

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

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)