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- EMDB-70174: Cryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70174
TitleCryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex
Map datafull map
Sample
  • Complex: AMT1-AMT7-AMTP1-AMTP2 complex
    • Protein or peptide: AMT7
    • Protein or peptide: mRNA m(6)A methyltransferase
    • Protein or peptide: Myb-like domain-containing protein
    • Protein or peptide: AMTP2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
Keywords6mA methyltransferase / TRANSFERASE
Function / homology
Function and homology information


mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / methylation / membrane / nucleus
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / Myb-like DNA-binding domain / SANT/Myb domain / Homeobox-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Transmembrane protein, putative / Uncharacterized protein / mRNA m(6)A methyltransferase / Myb-like domain-containing protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsSong J / Shao Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Protein Sci / Year: 2025
Title: Structural insight into the substrate binding of the AMT complex via an inhibitor-trapped state.
Authors: Zengyu Shao / Sol Yoon / Jiuwei Lu / Pranav Athavale / Yifan Liu / Jikui Song /
Abstract: N6-adenine (6mA) DNA methylation plays an important role in gene regulation and genome stability. The 6mA methylation in Tetrahymena thermophila is mainly mediated by the AMT complex, comprised of ...N6-adenine (6mA) DNA methylation plays an important role in gene regulation and genome stability. The 6mA methylation in Tetrahymena thermophila is mainly mediated by the AMT complex, comprised of the AMT1, AMT7, AMTP1, and AMTP2 subunits. To date, how this complex assembles on the DNA substrate remains elusive. Here we report the structure of the AMT complex bound to the OCR protein from bacteriophage T7, mimicking the AMT-DNA encounter complex. The AMT1-AMT7 heterodimer approaches OCR from one side, while the AMTP1 N-terminal domain, assuming a homeodomain fold, binds to OCR from the other side, resulting in a saddle-shaped architecture reminiscent of what was observed for prokaryotic 6mA writers. Mutation of the AMT1, AMT7, and AMTP1 residues on the OCR-contact points led to impaired DNA methylation activity to various extents, supporting a role for these residues in DNA binding. Furthermore, structural comparison of the AMT1-AMT7 subunits with the evolutionarily related METTL3-METTL14 and AMT1-AMT6 complexes reveals sequence conservation and divergence in the region corresponding to the OCR-binding site, shedding light on the substrate binding of the latter two complexes. Together, this study supports a model in which the AMT complex undergoes a substrate binding-induced open-to-closed conformational transition, with implications in its substrate binding and processive 6mA methylation.
History
DepositionApr 13, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70174.png

Downloads & links

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Map

FileDownload / File: emd_70174.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 200 pix.
= 271.36 Å		1.36 Å/pix.
x 200 pix.
= 271.36 Å		1.36 Å/pix.
x 200 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3568 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.87155896 - 1.6007539
Average (Standard dev.)0.0002382433 (±0.024589121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_70174_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_70174_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMT1-AMT7-AMTP1-AMTP2 complex

EntireName: AMT1-AMT7-AMTP1-AMTP2 complex
Components
  • Complex: AMT1-AMT7-AMTP1-AMTP2 complex
    • Protein or peptide: AMT7
    • Protein or peptide: mRNA m(6)A methyltransferase
    • Protein or peptide: Myb-like domain-containing protein
    • Protein or peptide: AMTP2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: AMT1-AMT7-AMTP1-AMTP2 complex

SupramoleculeName: AMT1-AMT7-AMTP1-AMTP2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)

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Macromolecule #1: AMT7

MacromoleculeName: AMT7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 52.08343 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGAPKKQEQE PIRLSTRTAS KKVDYLQLSN GKLEDFFDDL EEDNKPARNR SRSKKRGRKP LKKADSRSKT PSRVSNARGR SKSLGPRKT YPRKKNLSPD NQLSLLLKWR NDKIPLKSAS ETDNKCKVVN VKNIFKSDLS KYGANLQALF INALWKVKSR K EKEGLNIN ...String:
MGAPKKQEQE PIRLSTRTAS KKVDYLQLSN GKLEDFFDDL EEDNKPARNR SRSKKRGRKP LKKADSRSKT PSRVSNARGR SKSLGPRKT YPRKKNLSPD NQLSLLLKWR NDKIPLKSAS ETDNKCKVVN VKNIFKSDLS KYGANLQALF INALWKVKSR K EKEGLNIN DLSNLKIPLS LMKNGILFIW SEKEILGQIV EIMEQKGFTY IENFSIMFLG LNKCLQSINH KDEDSQNSTA ST NNTNNEA ITSDLTLKDT SKFSDQIQDN HSEDSDQARK QQTPDDITQK KNKLLKKSSV PSIQKLFEED PVQTPSVNKP IEK SIEQVT QEKKFVMNNL DILKSTDINN LFLRNNYPYF KKTRHTLLMF RRIGDKNQKL ELRHQRTSDV VFEVTDEQDP SKVD TMMKE YVYQMIETLL PKAQFIPGVD KHLKMMELFA STDNYRPGWI SVIEK

UniProtKB: Uncharacterized protein

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Macromolecule #2: mRNA m(6)A methyltransferase

MacromoleculeName: mRNA m(6)A methyltransferase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA m6A methyltransferase
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 42.696059 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSKAVNKKGL RPRKSDSILD HIKNKLDQEF LEDNENGEQS DEDYDQKSLN KAKKPYKKRQ TQNGSELVIS QQKTKAKASA NNKKSAKNS QKLDEEEKIV EEEDLSPQKN GAVSEDDQQQ EASTQEDDYL DRLPKSKKGL QGLLQDIEKR ILHYKQLFFK E QNEIANGK ...String:
MSKAVNKKGL RPRKSDSILD HIKNKLDQEF LEDNENGEQS DEDYDQKSLN KAKKPYKKRQ TQNGSELVIS QQKTKAKASA NNKKSAKNS QKLDEEEKIV EEEDLSPQKN GAVSEDDQQQ EASTQEDDYL DRLPKSKKGL QGLLQDIEKR ILHYKQLFFK E QNEIANGK RSMVPDNSIP ICSDVTKLNF QALIDAQMRH AGKMFDVIMM DPPWQLSSSQ PSRGVAIAYD SLSDEKIQNM PI QSLQQDG FIFVWAINAK YRVTIKMIEN WGYKLVDEIT WVKKTVNGKI AKGHGFYLQH AKESCLIGVK GDVDNGRFKK NIA SDVIFS ERRGQSQKPE EIYQYINQLC PNGNYLEIFA RRNNLHDNWV SIGNEL

UniProtKB: mRNA m(6)A methyltransferase

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Macromolecule #3: Myb-like domain-containing protein

MacromoleculeName: Myb-like domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 41.602758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSLKKGKFQH NQSKSLWNYT LSPGWREEEV KILKSALQLF GIGKWKKIME SGCLPGKSIG QIYMQTQRLL GQQSLGDFMG LQIDLEAVF NQNMKKQDVL RKNNCIINTG DNPTKEERKR RIEQNRKIYG LSAKQIAEIK LPKVKKHAPQ YMTLEDIENE K FTNLEILT ...String:
MSLKKGKFQH NQSKSLWNYT LSPGWREEEV KILKSALQLF GIGKWKKIME SGCLPGKSIG QIYMQTQRLL GQQSLGDFMG LQIDLEAVF NQNMKKQDVL RKNNCIINTG DNPTKEERKR RIEQNRKIYG LSAKQIAEIK LPKVKKHAPQ YMTLEDIENE K FTNLEILT HLYNLKAEIV RRLAEQGETI AQPSIIKSLN NLNHNLEQNQ NSNSSTETKV TLEQSGKKKY KVLAIEETEL QN GPIATNS QKKSINGKRK NNRKINSDSE GNEEDISLED IDSQESEINS EEIVEDDEED EQIEEPSKIK KRKKNPEQES EED DIEEDQ EEDELVVNEE EIFEDDDDDE DNQDSSEDDD DDED

UniProtKB: Myb-like domain-containing protein

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Macromolecule #4: AMTP2

MacromoleculeName: AMTP2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 16.612893 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKKNGKSQNQ PLDFTQYAKN MRKDLSNQDI CLEDGALNHS YFLTKKGQYW TPLNQKALQR GIELFGVGNW KEINYDEFSG KANIVELEL RTCMILGIND ITEYYGKKIS EEEQEEIKKS NIAKGKKENK LKDNIYQKLQ QMQ

UniProtKB: Transmembrane protein, putative

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Macromolecule #5: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.55 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66922
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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