SAXSdb — 9u9k

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1. Structure Basics

entry_id	9u9k
deposition_date	2025-03-28
last_revision	2025-11-05
title	Cryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B)
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	31.85 Å
rg_electron	31.61 Å
i0	143998000.00
molecular_weight	88826.0 kDa
excluded_volume	108350 Å³
envelope_volume	145310 Å³
shell_volume	39044 Å³
envelope_diameter	110.2 Å
shell_rg	37.77 Å
envelope_rg	31.73 Å
shape_rg	31.60 Å
total_rg	32.12 Å
total_atoms	6205
n_residues	696
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	104.3 Å
rg_real	31.86 Å
rg_real_error	0.73 Å
i0_real	1.4400e+08
i0_real_error	2.0870e+06
rg_reciprocal	31.86 Å
i0_reciprocal	144000000.0000
total_estimate	0.8799
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.6 Å
skewness	0.385
kurtosis	-0.126
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	19030000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.824

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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	6205

GPEFKLMSKAVNKKGLRPRKSDSILDHIKNKLDQEFLEDNENGEQSDEDYDQKSLNKAKKPYKKRQTQNGSELVISQQKTKAKASANNKKSAKNSQKLDEEEKIVEEEDLSPQKNGAVSEDDQQQEASTQEDDYLDRLPKSKKGLQGLLQDIEKRILHYKQLFFKEQNEIANGKRSMVPDNSIPICSDVTKLNFQALIDAQMRHAGKMFDVIMMDPPWQLSSSQPSRGVAIAYDSLSDEKIQNMPIQSLQQDGFIFVWAINAKYRVTIKMIENWGYKLVDEITWVKKTVNGKIAKGHGFYLQHAKESCLIGVKGDVDNGRFKKNIASDVIFSERRGQSQKPEEIYQYINQLCPNGNYLEIFARRNNLHDNWVSIGNEL

Source

organism	Tetrahymena thermophila SB210
ncbi_taxonomy_id	312017
host_organism	Escherichia coli

Entity 2 polymer

description	Methyltransferase MT, putative
formula_weight	41270.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPGRPMSQETLAACQSLDKFAHPKKVSPVQKSQIIEEPPLQKKIKPTEPGEDQLSLLLKWRSSYIPPQKPTNEDEYKKIICKDISSEKLEQHAGDVSALFINIKWKLSEGQSGKSIEDLKKLAISDKLINNGIIFIWSEKEILSQIVDVLEAKGFNYIENFMINQLSADKALEMQRKNQNQQSKEKKITDFFKRLTPQKNIWSDITPEQCIEQEKFPPNNYVQDIFVNSEYSFFRKSKKILLMLRKFNKDAQLELRHQRTSDIFFDIFEQNKPNDVSKKGMEFVYKMIETLLPKANYSEENKGAFKMMELYADDKSQPRKGWISVYEQEWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

AGTTAAAGTTAAGATGTTAAGAAAGTT

Entity 6 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	F

AACTTTCTTAACATCTTAACTTTAACT

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	2.96 Å
resolution_method	—
num_particles	335709

fit	/app/data/saxs_computation/u9/9u9k/9u9k.fit
pddf	/app/data/pr_computation/u9/9u9k/9u9k.pr.out
profile	/app/data/saxs_computation/u9/9u9k/9u9k.dat

Cryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B)

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

Entity 6 polymer

Polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)