9u9k

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

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

mRNA m(6)A methyltransferase

Tetrahymena thermophila SB210

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	Methyltransferase MT, putative × 1 （Q22XT1） Myb-like DNA-binding domain protein × 1 （Q22VV9） Transmembrane protein, putative × 1 （I7M8B9） DNA (27-MER) × 1 DNA (27-MER) × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q22GC0_TETTS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–378； UniProt 57–428

Methyltransferase MT, putative

Tetrahymena thermophila SB210

UniProt Q22XT1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	mRNA m(6)A methyltransferase × 1 （Q22GC0） Myb-like DNA-binding domain protein × 1 （Q22VV9） Transmembrane protein, putative × 1 （I7M8B9） DNA (27-MER) × 1 DNA (27-MER) × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q22XT1_TETTS
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–329； UniProt 1–324

Myb-like DNA-binding domain protein

Tetrahymena thermophila SB210

UniProt Q22VV9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	mRNA m(6)A methyltransferase × 1 （Q22GC0） Methyltransferase MT, putative × 1 （Q22XT1） Transmembrane protein, putative × 1 （I7M8B9） DNA (27-MER) × 1 DNA (27-MER) × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q22VV9_TETTS
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–364； UniProt 2–360

Transmembrane protein, putative

Tetrahymena thermophila SB210

UniProt I7M8B9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	mRNA m(6)A methyltransferase × 1 （Q22GC0） Methyltransferase MT, putative × 1 （Q22XT1） Myb-like DNA-binding domain protein × 1 （Q22VV9） DNA (27-MER) × 1 DNA (27-MER) × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I7M8B9_TETTS
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 5–146； UniProt 154–295

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9u9k
Deposition date deposition_date	2025-03-28
Last revision last_revision	2025-11-05
Structure title title	Cryo-EM structure of hemi-methylated DNA-bound Tetrahymena DNA methyltransferase complex MTA1c (MTA9-B)
Keywords 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
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9u9k__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9u9k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9u9k__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.85 Å
Rg (electron density)	31.61 Å
Total Rg	32.12 Å
Atom count	6205
Residues	696
Excluded volume	108350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9u9k__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	mRNA m(6)A methyltransferase
Molecular weight formula_weight	43368.9 kDa
EC 编号 ec_number	2.1.1.348
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6205

GPEFKLMSKAVNKKGLRPRKSDSILDHIKNKLDQEFLEDNENGEQSDEDYDQKSLNKAKKPYKKRQTQNGSELVISQQKTKAKASANNKKSAKNSQKLDEEEKIVEEEDLSPQKNGAVSEDDQQQEASTQEDDYLDRLPKSKKGLQGLLQDIEKRILHYKQLFFKEQNEIANGKRSMVPDNSIPICSDVTKLNFQALIDAQMRHAGKMFDVIMMDPPWQLSSSQPSRGVAIAYDSLSDEKIQNMPIQSLQQDGFIFVWAINAKYRVTIKMIENWGYKLVDEITWVKKTVNGKIAKGHGFYLQHAKESCLIGVKGDVDNGRFKKNIASDVIFSERRGQSQKPEEIYQYINQLCPNGNYLEIFARRNNLHDNWVSIGNEL

Source Source

Source organism organism	Tetrahymena thermophila SB210
NCBI taxonomy ID ncbi_taxonomy_id	312017
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Methyltransferase MT, putative
Molecular weight formula_weight	41270.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPGRPMSQETLAACQSLDKFAHPKKVSPVQKSQIIEEPPLQKKIKPTEPGEDQLSLLLKWRSSYIPPQKPTNEDEYKKIICKDISSEKLEQHAGDVSALFINIKWKLSEGQSGKSIEDLKKLAISDKLINNGIIFIWSEKEILSQIVDVLEAKGFNYIENFMINQLSADKALEMQRKNQNQQSKEKKITDFFKRLTPQKNIWSDITPEQCIEQEKFPPNNYVQDIFVNSEYSFFRKSKKILLMLRKFNKDAQLELRHQRTSDIFFDIFEQNKPNDVSKKGMEFVYKMIETLLPKANYSEENKGAFKMMELYADDKSQPRKGWISVYEQEWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source Source

Source organism organism	Tetrahymena thermophila SB210
NCBI taxonomy ID ncbi_taxonomy_id	312017
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Myb-like DNA-binding domain protein
Molecular weight formula_weight	41937.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPGRPSLKKGKFQHNQSKSLWNYTLSPGWREEEVKILKSALQLFGIGKWKKIMESGCLPGKSIGQIYMQTQRLLGQQSLGDFMGLQIDLEAVFNQNMKKQDVLRKNNCIINTGDNPTKEERKRRIEQNRKIYGLSAKQIAEIKLPKVKKHAPQYMTLEDIENEKFTNLEILTHLYNLKAEIVRRLAEQGETIAQPSIIKSLNNLNHNLEQNQNSNSSTETKVTLEQSGKKKYKVLAIEETELQNGPIATNSQKKSINGKRKNNRKINSDSEGNEEDISLEDIDSQESEINSEEIVEDDEEDEQIEEPSKIKKRKKNPEQESEEDDIEEDQEEDELVVNEEEIFEDDDDDEDNQDSSEDDDDDED

Source Source

Source organism organism	Tetrahymena thermophila SB210
NCBI taxonomy ID ncbi_taxonomy_id	312017
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Transmembrane protein, putative
Molecular weight formula_weight	17043.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GPEFMKKNGKSQNQPLDFTQYAKNMRKDLSNQDICLEDGALNHSYFLTKKGQYWTPLNQKALQRGIELFGVGNWKEINYDEFSGKANIVELELRTCMILGINDITEYYGKKISEEEQEEIKKSNIAKGKKENKLKDNIYQKLQQMQ

Source Source

Source organism organism	Tetrahymena thermophila SB210
NCBI taxonomy ID ncbi_taxonomy_id	312017
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (27-MER)
Molecular weight formula_weight	8426.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AGTTAAAGTTAAGATGTTAAGAAAGTT

Entity 6 Entity 6 polymer

Description description	DNA (27-MER)
Molecular weight formula_weight	8173.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AACTTTCTTAACATCTTAACTTTAACT

Entity 7 Entity 7 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.96 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	335709

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

mRNA m(6)A methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methyltransferase MT, putative

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Myb-like DNA-binding domain protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transmembrane protein, putative

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9u9k__assembly_1__model_1

9u9k__assembly_1__model_1 | I(q)

9u9k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)