[English] 日本語
Yorodumi
- EMDB-60984: Iterative acetyltransferase on lasso peptides from Actinomycetes ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60984
TitleIterative acetyltransferase on lasso peptides from Actinomycetes in complex with AcCoA
Map data
Sample
  • Complex: Complex of iterative acetyltransferase and AcCoA
    • Complex: Iterative acetyltransferase
      • Protein or peptide: GCN5-related N-acetyltransferase
  • Ligand: ACETYL COENZYME *A
KeywordsGCN5-related N-acetyltransferases / Actinomycetes / AcCoA / TRANSFERASE
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / GCN5-related N-acetyltransferase
Function and homology information
Biological speciesActinosynnema mirum DSM 43827 (bacteria) / Actinomycetes (high G+C Gram-positive bacteria) / Actinosynnema mirum (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsWu S / Xiong J / Lei D / Dong S
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077056 China
National Natural Science Foundation of China (NSFC)22377046 China
National Natural Science Foundation of China (NSFC)32171300 China
National Natural Science Foundation of China (NSFC)2210070084 China
National Natural Science Foundation of China (NSFC)21907046 China
Other government22ZD6FA006
Other government23ZDFA015
CitationJournal: To Be Published
Title: Iterative acylation on mature lasso peptides by widespread GNATs for lipolasso production
Authors: Xiong J / Wu S / Liang Z / Gong X / Fang S / Tao F / Wu Q / Cui J / Gao K / Luo S / Lei D / Dong S
History
DepositionJul 29, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60984.png

Downloads & links

-
Map

FileDownload / File: emd_60984.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.736 Å		0.83 Å/pix.
x 256 pix.
= 212.736 Å		0.83 Å/pix.
x 256 pix.
= 212.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.319
Minimum - Maximum-0.039043948 - 2.6327431
Average (Standard dev.)0.008993944 (±0.0937268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.736 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_60984_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60984_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60984_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of iterative acetyltransferase and AcCoA

EntireName: Complex of iterative acetyltransferase and AcCoA
Components
  • Complex: Complex of iterative acetyltransferase and AcCoA
    • Complex: Iterative acetyltransferase
      • Protein or peptide: GCN5-related N-acetyltransferase
  • Ligand: ACETYL COENZYME *A

-
Supramolecule #1: Complex of iterative acetyltransferase and AcCoA

SupramoleculeName: Complex of iterative acetyltransferase and AcCoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)

-
Supramolecule #2: Iterative acetyltransferase

SupramoleculeName: Iterative acetyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Actinomycetes (high G+C Gram-positive bacteria)

-
Macromolecule #1: GCN5-related N-acetyltransferase

MacromoleculeName: GCN5-related N-acetyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Actinosynnema mirum (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101) (bacteria)
Molecular weightTheoretical: 21.676164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPQDDLIVW LRGDRAGLGP FSADLVDQYW RWEQDPSVLI GYGRQTPDSL ENRREGYGHQ ARGTDDQLRF TVYDLTGQDP VPVGTTAVL IDHHVRTGEF VIQLGAGHRG RGLGTEATRL TLDYAFHVSA LACVHLAVLT PNTGAIAAYE RAGFRRIGER R DSGFWLGR ...String:
MSPQDDLIVW LRGDRAGLGP FSADLVDQYW RWEQDPSVLI GYGRQTPDSL ENRREGYGHQ ARGTDDQLRF TVYDLTGQDP VPVGTTAVL IDHHVRTGEF VIQLGAGHRG RGLGTEATRL TLDYAFHVSA LACVHLAVLT PNTGAIAAYE RAGFRRIGER R DSGFWLGR RVSETLMDAV PEDFPGPSVV RGFVEGGR

UniProtKB: GCN5-related N-acetyltransferase

-
Macromolecule #2: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 4350000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
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