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9z2n

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (D-arm conformation)

Method: ELECTRON MICROSCOPY D_max: 91.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z2n
deposition_date	2025-11-05
title	CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (D-arm conformation)
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	29.10 Å
rg_electron	28.34 Å
i0	325356000.00
molecular_weight	87773.0 kDa
excluded_volume	80174 Å³
envelope_volume	146180 Å³
shell_volume	41760 Å³
envelope_diameter	96.0 Å
shell_rg	36.72 Å
envelope_rg	28.31 Å
shape_rg	28.30 Å
total_rg	28.94 Å
total_atoms	6481
n_residues	675
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	28.97 Å
rg_real_error	0.51 Å
i0_real	3.2540e+08
i0_real_error	4.6610e+06
rg_reciprocal	29.03 Å
i0_reciprocal	325400000.0000
total_estimate	0.8970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.6 Å
skewness	0.217
kurtosis	-0.396
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	25710000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.980

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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	6481

MHHHHHHENLYFQGSGGRRSRGRRLQQQQRPEDAEDGAEGGGKRGEAGWEGGYPEIVKENKLFEHYYQELKIVPEGEWGQFMDALREPLPATLRITGYKSHAKEILHCLKNKYFKELEDLEVDGQKVEVPQPLSWYPEELAWHTNLSRKILRKSPHLEKFHQFLVSETESGNISRQEAVSMIPPLLLNVRPHHKILDMCAAPGSKTTQLIEMLHADMNVPFPEGFVIANDVDNKRCYLLVHQAKRLSSPCIMVVNHDASSIPRLQIDVDGRKEILFYDRILCDVPASGDGTMRKNIDVWKKWTTLNSLQLHGLQLRIATRGAEQLAEGGRMVYSTCSLNPIEDEAVIASLLEKSEGALELADVSNELPGLKWMPGITQWKVMTKDGQWFTDWDAVPHSRHTQIRPTMFPPKDPEKLQAMHLERCLRILPHHQNTGGFFVAVLVKKSSMPWNKRQPKLQGKSAETRESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSKKDGVCGPPPSKKMKLFGFKEDPFVFIPEDDPLFPPIEKFYALDPSFPRMNLLTRTTEGKKRQLYMVSKELRNVLLNNSEKMKVINTGIKVWCRNNSGEEFDCAFRLAQEGIYTLYPFINSRIITVSMEDVKILLTQENPFFRKLSSETYSQAKDLAKGSIVLKYEPDSANPDALQCPIVLCGWRGKASIRTFVPKNERLHYLRMMGLEVLGEKKKEGVILTNESAASTGQPDNDVTEGQRAGEPNSPDAEEANSPDVTAGCDPAGVHPPR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	tRNA Lys(CTT)
formula_weight	24508.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

GCCCGGCUAGCUCAGUCGGUAGAGCAUGGGACUCUUAAUCCCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCCA

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	triclinic

resolution	2.570 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.57 Å
resolution_method	—
num_particles	243000

fit	/app/data/saxs_computation/z2/9z2n/9z2n.fit
pddf	/app/data/pr_computation/z2/9z2n/9z2n.pr.out
profile	/app/data/saxs_computation/z2/9z2n/9z2n.dat

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (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)