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9z2u

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

Method: ELECTRON MICROSCOPY D_max: 91.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z2u
deposition_date	2025-11-05
title	CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (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	28.91 Å
rg_electron	28.21 Å
i0	314485000.00
molecular_weight	86312.0 kDa
excluded_volume	78888 Å³
envelope_volume	144050 Å³
shell_volume	41483 Å³
envelope_diameter	96.0 Å
shell_rg	36.52 Å
envelope_rg	28.08 Å
shape_rg	28.17 Å
total_rg	28.79 Å
total_atoms	6372
n_residues	663
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	91.0 Å
rg_real	28.79 Å
rg_real_error	0.56 Å
i0_real	3.1450e+08
i0_real_error	4.3710e+06
rg_reciprocal	28.85 Å
i0_reciprocal	314500000.0000
total_estimate	0.8961
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.8 Å
skewness	0.244
kurtosis	-0.346
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	30210000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.963

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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	6372

MHHHHHHENLYFQGSGGRRSRGRRLQQQQRPEDAEDGAEGGGKRGEAGWEGGYPEIVKENKLFEHYYQELKIVPEGEWGQFMDALREPLPATLRITGYKSHAKEILHCLKNKYFKELEDLEVDGQKVEVPQPLSWYPEELAWHTNLSRKILRKSPHLEKFHQFLVSETESGNISRQEAVSMIPPLLLNVRPHHKILDMCAAPGSKTTQLIEMLHADMNVPFPEGFVIANDVDNKRCYLLVHQAKRLSSPCIMVVNHDASSIPRLQIDVDGRKEILFYDRILCDVPASGDGTMRKNIDVWKKWTTLNSLQLHGLQLRIATRGAEQLAEGGRMVYSTCSLNPIEDEAVIASLLEKSEGALELADVSNELPGLKWMPGITQWKVMTKDGQWFTDWDAVPHSRHTQIRPTMFPPKDPEKLQAMHLERCLRILPHHQNTGGFFVAVLVKKSSMPWNKRQPKLQGKSAETRESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSKKDGVCGPPPSKKMKLFGFKEDPFVFIPEDDPLFPPIEKFYALDPSFPRMNLLTRTTEGKKRQLYMVSKELRNVLLNNSEKMKVINTGIKVWCRNNSGEEFDCAFRLAQEGIYTLYPFINSRIITVSMEDVKILLTQENPFFRKLSSETYSQAKDLAKGSIVLKYEPDSANPDALQCPIVLCGWRGKASIRTFVPKNERLHYLRMMGLEVLGEKKKEGVILTNESAASTGQPDNDVTEGQRAGEPNSPDAEEANSPDVTAGCDPAGVHPPR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	tRNA Lys(TTT)
formula_weight	24433.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

GCCUGGAUAGCUCAGUUGGUAGAACAUCAGACUUUUAAUCUGACGGUGCAGGGUUCAAGUCCCUGUUCAGGCGCCA

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	3.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.00 Å
resolution_method	—
num_particles	239000

fit	/app/data/saxs_computation/z2/9z2u/9z2u.fit
pddf	/app/data/pr_computation/z2/9z2u/9z2u.pr.out
profile	/app/data/saxs_computation/z2/9z2u/9z2u.dat

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