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9v4p

Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA

Method: ELECTRON MICROSCOPY D_max: 104.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v4p
deposition_date	2025-05-24
last_revision	2025-11-26
title	Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA
keywords	DNA methylation, MET1, Cryo-EM structure, epigenetic regulation, GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/DNA
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	31.31 Å
rg_electron	30.68 Å
i0	174658000.00
molecular_weight	97947.0 kDa
excluded_volume	119500 Å³
envelope_volume	159640 Å³
shell_volume	42992 Å³
envelope_diameter	110.6 Å
shell_rg	37.99 Å
envelope_rg	30.94 Å
shape_rg	30.64 Å
total_rg	31.43 Å
total_atoms	6850
n_residues	807
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	104.0 Å
rg_real	31.24 Å
rg_real_error	0.80 Å
i0_real	1.7470e+08
i0_real_error	2.8660e+06
rg_reciprocal	31.27 Å
i0_reciprocal	174700000.0000
total_estimate	0.8887
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.7 Å
skewness	0.303
kurtosis	-0.284
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	32590000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	;DNA (5'-D(TPAPATPGPAPCPAPTPAP(5CM)PGPAPTPCPCPAPAPTPC)-3') ;
formula_weight	6100.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B
atom_count	6851

TAATGACATACGATCCAATC

Entity 2 polymer

description	;DNA (5'-D(GPAPTPTPGPGPAPTP(C49)PGPTPAPTPGPTPCPAPTPTPA)-3') ;
formula_weight	6243.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

GATTGGATCGTATGTCATTA

Entity 3 polymer

description	DNA (cytosine-5)-methyltransferase 1
formula_weight	103673.6 kDa
ec_number	2.1.1.37
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

SNPRAGMAPVASKRKAMQATTTRLVNRIWGEFYSNYSPEDPLQATAAENGEDEVEEEGGNGEEEVEEEGENGLTEDTVPEPVEVQKPHTPKKIRGSSGKREIKWDGESLGKTSAGEPLYQQALVGGEMVAVGGAVTLEVDDPDEMPAIYFVEYMFESTDHCKMLHGRFLQRGSMTVLGNAANERELFLTNECMTTQLKDIKGVASFEIRSRPWGHQYRKKNITADKLDWARALERKVKDLPTEYYCKSLYSPERGGFFSLPLSDIGRSSGFCTSCKIREDEEKRSTIKLNVSKTGFFINGIEYSVEDFVYVNPDSIGGLKEGSKTSFKSGRNIGLRAYVVCQLLEIVPKESRKADLGSFDVKVRRFYRPEDVSAEKAYASDIQELYFSQDTVVLPPGALEGKCEVRKKSDMPLSREYPISDHIFFCDLFFDTSKGSLKQLPANMKPKFSTIKDDTLLRKKKGKGVESEIESEIVKPVEPPKEIRLATLDIFAGCGGLSHGLKKAGVSDAKWAIEYEEPAGQAFKQNHPESTVFVDNCNVILRAIMEKGGDQDDCVSTTEANELAAKLTEEQKSTLPLPGQVDFINGGPPCQGFSGMNRFNQSSWSKVQCEMILAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFGILEAGAYGVSQSRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLHYAAVRSTALGAPFRPITVRDTIGDLPSVENGDSRTNKEYKEVAVSWFQKEIRGNTIALTDHICKAMNELNLIRCKLIPTRPGADWHDLPKRKVTLSDGRVEEMIPFCLPNTAERHNGWKGLYGRLDWQGNFPTSVTDPQPMGKVGMCFHPEQHRILTVRECARSQGFPDSYEFAGNINHKHRQIGNAVPPPLAFALGRKLKEALHLKKSPQHQP

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 4 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	nat
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	2.34 Å
resolution_method	—
num_particles	861458

fit	/app/data/saxs_computation/v4/9v4p/9v4p.fit
pddf	/app/data/pr_computation/v4/9v4p/9v4p.pr.out
profile	/app/data/saxs_computation/v4/9v4p/9v4p.dat

Cryo-EM structure of A. thaliana MET1(610-1534) bound covalently to a hemi-mCpG DNA

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)