SAXSdb — 9u9e

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1. Structure Basics

entry_id	9u9e
deposition_date	2025-03-27
last_revision	2025-11-05
title	Cryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c
keywords	;DNA methyltransferase, DNA N6-methyladenine modification, protein-DNA complex, chromatin regulation, gene regulation, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/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	31.90 Å
rg_electron	31.51 Å
i0	212757000.00
molecular_weight	108660.0 kDa
excluded_volume	132770 Å³
envelope_volume	174400 Å³
shell_volume	45150 Å³
envelope_diameter	111.3 Å
shell_rg	39.12 Å
envelope_rg	31.77 Å
shape_rg	31.50 Å
total_rg	32.14 Å
total_atoms	7580
n_residues	852
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	103.7 Å
rg_real	31.78 Å
rg_real_error	0.70 Å
i0_real	2.1280e+08
i0_real_error	3.0520e+06
rg_reciprocal	31.83 Å
i0_reciprocal	212800000.0000
total_estimate	0.8863
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.5 Å
skewness	0.260
kurtosis	-0.262
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	31560000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.920

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	mRNA m(6)A methyltransferase
formula_weight	43368.9 kDa
ec_number	2.1.1.348
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7580

GPEFKLMSKAVNKKGLRPRKSDSILDHIKNKLDQEFLEDNENGEQSDEDYDQKSLNKAKKPYKKRQTQNGSELVISQQKTKAKASANNKKSAKNSQKLDEEEKIVEEEDLSPQKNGAVSEDDQQQEASTQEDDYLDRLPKSKKGLQGLLQDIEKRILHYKQLFFKEQNEIANGKRSMVPDNSIPICSDVTKLNFQALIDAQMRHAGKMFDVIMMDPPWQLSSSQPSRGVAIAYDSLSDEKIQNMPIQSLQQDGFIFVWAINAKYRVTIKMIENWGYKLVDEITWVKKTVNGKIAKGHGFYLQHAKESCLIGVKGDVDNGRFKKNIASDVIFSERRGQSQKPEEIYQYINQLCPNGNYLEIFARRNNLHDNWVSIGNEL

Source

organism	Tetrahymena thermophila SB210
ncbi_taxonomy_id	312017
host_organism	Escherichia coli

Entity 2 polymer

description	MT-a70 family protein MTA9
formula_weight	55576.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPGRPMAPKKQEQEPIRLSTRTASKKVDYLQLSNGKLEDFFDDLEEDNKPARNRSRSKKRGRKPLKKADSRSKTPSRVSNARGRSKSLGPRKTYPRKKNLSPDNQLSLLLKWRNDKIPLKSASETDNKCKVVNVKNIFKSDLSKYGANLQALFINALWKVKSRKEKEGLNINDLSNLKIPLSLMKNGILFIWSEKEILGQIVEIMEQKGFTYIENFSIMFLGLNKCLQSINHKDEDSQNSTASTNNTNNEAITSDLTLKDTSKFSDQIQDNHSEDSDQARKQQTPDDITQKKNKLLKKSSVPSIQKLFEEDPVQTPSVNKPIEKSIEQVTQEKKFVMNNLDILKSTDINNLFLRNNYPYFKKTRHTLLMFRRIGDKNQKLELRHQRTSDVVFEVTDEQDPSKVDTMMKEYVYQMIETLLPKAQFIPGVDKHLKMMELFASTDNYRPGWISVIEKGAPWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source

organism	Tetrahymena thermophila SB210
ncbi_taxonomy_id	312017
host_organism	Escherichia coli

Entity 3 polymer

description	Myb-like DNA-binding domain protein
formula_weight	41937.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GPGRPSLKKGKFQHNQSKSLWNYTLSPGWREEEVKILKSALQLFGIGKWKKIMESGCLPGKSIGQIYMQTQRLLGQQSLGDFMGLQIDLEAVFNQNMKKQDVLRKNNCIINTGDNPTKEERKRRIEQNRKIYGLSAKQIAEIKLPKVKKHAPQYMTLEDIENEKFTNLEILTHLYNLKAEIVRRLAEQGETIAQPSIIKSLNNLNHNLEQNQNSNSSTETKVTLEQSGKKKYKVLAIEETELQNGPIATNSQKKSINGKRKNNRKINSDSEGNEEDISLEDIDSQESEINSEEIVEDDEEDEQIEEPSKIKKRKKNPEQESEEDDIEEDQEEDELVVNEEEIFEDDDDDEDNQDSSEDDDDDED

Source

organism	Tetrahymena thermophila SB210
ncbi_taxonomy_id	312017
host_organism	Escherichia coli

Entity 4 polymer

description	Transmembrane protein, putative
formula_weight	17043.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

GPEFMKKNGKSQNQPLDFTQYAKNMRKDLSNQDICLEDGALNHSYFLTKKGQYWTPLNQKALQRGIELFGVGNWKEINYDEFSGKANIVELELRTCMILGINDITEYYGKKISEEEQEEIKKSNIAKGKKENKLKDNIYQKLQQMQ

Source

organism	Tetrahymena thermophila SB210
ncbi_taxonomy_id	312017
host_organism	Escherichia coli

Entity 5 polymer

description	DNA (27-MER)
formula_weight	8426.5 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

AGTTAAAGTTAAGATGTTAAGAAAGTT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	synthetic construct

Entity 6 polymer

description	DNA (27-MER)
formula_weight	8173.3 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

AACTTTCTTAACATCTTAACTTTAACT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	synthetic construct

Entity 7 non-polymer

description	S-ADENOSYLMETHIONINE
formula_weight	398.4 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	2.89 Å
resolution_method	—
num_particles	203776

fit	/app/data/saxs_computation/u9/9u9e/9u9e.fit
pddf	/app/data/pr_computation/u9/9u9e/9u9e.pr.out
profile	/app/data/saxs_computation/u9/9u9e/9u9e.dat

Cryo-EM structure of hemimethylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)