[English] 日本語
Yorodumi
- EMDB-70174: Cryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex -

+
Open data


ID or keywords:

Loading...

-
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 / nucleus / membrane
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: To Be Published
Title: Cryo-EM structure of AMT1-AMT7-AMTP1-AMTP2 complex
Authors: Song J / Shao Z
History
DepositionApr 13, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
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
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 °

-
Supplemental data

-
Half map: half map

Fileemd_70174_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: half map

Fileemd_70174_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more