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9q7u

Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome

Method: ELECTRON MICROSCOPY D_max: 178.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q7u
deposition_date	2025-08-25
title	Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome
keywords	DNMT3A2-DNMT3B3, DNA methylation, 167H3K36me2-nucleosome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	55.43 Å
rg_electron	55.28 Å
i0	2738790000.00
molecular_weight	370270.0 kDa
excluded_volume	434590 Å³
envelope_volume	718120 Å³
shell_volume	105930 Å³
envelope_diameter	183.1 Å
shell_rg	61.31 Å
envelope_rg	53.08 Å
shape_rg	55.28 Å
total_rg	55.40 Å
total_atoms	48116
n_residues	2682
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	178.1 Å
rg_real	55.25 Å
rg_real_error	1.52 Å
i0_real	2.7390e+09
i0_real_error	6.2540e+07
rg_reciprocal	55.56 Å
i0_reciprocal	2740000000.0000
total_estimate	0.8855
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.0 Å
skewness	0.155
kurtosis	-0.565
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	244000000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.724

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Histone H3
formula_weight	15331.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	48116

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H2A type 1
formula_weight	13978.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B 1.1
formula_weight	13655.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 5 polymer

description	DNA (162-MER)
formula_weight	51786.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCGGCCGCCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGAT

Entity 6 polymer

description	DNA (162-MER)
formula_weight	51327.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGGCGGCCGAT

Entity 7 polymer

description	Isoform 7 of DNA (cytosine-5)-methyltransferase 3B
formula_weight	65568.4 kDa
ec_number	2.1.1.37
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	V,Z

DSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEKDYDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera

Entity 8 polymer

description	DNA (cytosine-5)-methyltransferase 3A
formula_weight	77914.7 kDa
ec_number	2.1.1.37
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,L

MNAVEENQGPGESQKVEEASPPAVQQPTDPASPTVATTPEPVGSDAGDKNATKAGDDEPEYEDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSRAGKLFPVCHDSDESDTAKAVEVQNKPMIEWALGGFQPSGPKGLEPPEEEKNPYKEVYTDMWVEPEAAAYAPPPPAKKPRKSTAEKPKVKEIIDERTRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera

Entity 9 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	9

Entity 10 non-polymer

description	5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
formula_weight	385.4 kDa
src_method	syn
entity_count	2

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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	3.40 Å
resolution_method	—
num_particles	652144

fit	/app/data/saxs_computation/q7/9q7u/9q7u.fit
pddf	/app/data/pr_computation/q7/9q7u/9q7u.pr.out
profile	/app/data/saxs_computation/q7/9q7u/9q7u.dat

Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome

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 (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 non-polymer

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)