[English] 日本語
Yorodumi
- EMDB-15790: Cryo-EM structure apolipoprotein N-acyltransferase Lnt from E.col... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15790
TitleCryo-EM structure apolipoprotein N-acyltransferase Lnt from E.coli in complex with FP3
Map data
Sample
  • Organelle or cellular component: Apolipoprotein N-acyltransferase
    • Protein or peptide: Apolipoprotein N-acyltransferase
  • Ligand: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate
KeywordsLnt / apolipoprotein N-acyltransferase / bacterial lipoprotein / transferase / cryo-EM
Function / homology
Function and homology information


apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Apolipoprotein N-acyltransferase, N-terminal / Apolipoprotein N-acyltransferase N-terminal domain / Apolipoprotein N-acyltransferase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsDegtjarik O / Smithers L / Boland C / Caffrey M / Shalev Benami M
Funding support Ireland, 2 items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
Irish Research CouncilGOIPD/2021/40 Ireland
CitationJournal: Sci Adv / Year: 2023
Title: Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein -acyltransferase.
Authors: Luke Smithers / Oksana Degtjarik / Dietmar Weichert / Chia-Ying Huang / Coilín Boland / Katherine Bowen / Abraham Oluwole / Corinne Lutomski / Carol V Robinson / Eoin M Scanlan / Meitian ...Authors: Luke Smithers / Oksana Degtjarik / Dietmar Weichert / Chia-Ying Huang / Coilín Boland / Katherine Bowen / Abraham Oluwole / Corinne Lutomski / Carol V Robinson / Eoin M Scanlan / Meitian Wang / Vincent Olieric / Moran Shalev-Benami / Martin Caffrey /
Abstract: Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP ...Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein -acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects.
History
DepositionSep 7, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15790.png

Downloads & links

-
Map

FileDownload / File: emd_15790.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.826 Å
Density
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-0.68076235 - 1.3057364
Average (Standard dev.)0.0005210767 (±0.035813324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.23999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_15790_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15790_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15790_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Apolipoprotein N-acyltransferase

EntireName: Apolipoprotein N-acyltransferase
Components
  • Organelle or cellular component: Apolipoprotein N-acyltransferase
    • Protein or peptide: Apolipoprotein N-acyltransferase
  • Ligand: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate

-
Supramolecule #1: Apolipoprotein N-acyltransferase

SupramoleculeName: Apolipoprotein N-acyltransferase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: Apolipoprotein N-acyltransferase

MacromoleculeName: Apolipoprotein N-acyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: apolipoprotein N-acyltransferase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 59.264703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MAFASLIERQ RIRLLLALLF GACGTLAFSP YDVWPAAIIS LMGLQALTFN RRPLQSAAIG FCWGFGLFG SGINWVYVSI ATFGGMPGPV NIFLVVLLAA YLSLYTGLFA GVLSRLWPKT TWLRVAIAAP ALWQVTEFLR G WVLTGFPW ...String:
MGSSHHHHHH SSGLVPRGSH MAFASLIERQ RIRLLLALLF GACGTLAFSP YDVWPAAIIS LMGLQALTFN RRPLQSAAIG FCWGFGLFG SGINWVYVSI ATFGGMPGPV NIFLVVLLAA YLSLYTGLFA GVLSRLWPKT TWLRVAIAAP ALWQVTEFLR G WVLTGFPW LQFGYSQIDG PLKGLAPIMG VEAINFLLMM VSGLLALALV KRNWRPLVVA VVLFALPFPL RYIQWFTPQP EK TIQVSMV QGDIPQSLKW DEGQLLNTLK IYYNATAPLM GKSSLIIWPE SAITDLEINQ QPFLKALDGE LRDKGSSLVT GIV DARLNK QNRYDTYNTI ITLGKGAPYS YESADRYNKN HLVPFGEFVP LESILRPLAP FFDLPMSSFS RGPYIQPPLS ANGI ELTAA ISYEIILGEQ VRDNFRPDTD YLLTISNDAW FGKSIGPWQH FQMARMRALE LARPLLRSTN NGITAVIGPQ GEIQA MIPQ FTREVLTTNV TPTTGLTPYA RTGNWPLWVL TALFGFAAVL MSLRQRRK

-
Macromolecule #2: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-ami...

MacromoleculeName: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1- ...Name: [(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate
type: ligand / ID: 2 / Number of copies: 1 / Formula: OJF
Molecular weightTheoretical: 1.330926 KDa
Chemical component information

ChemComp-OJF:
[(2~{R})-3-[(2~{R})-3-[[(2~{R})-1-[[(2~{R})-1-[[(2~{R})-6-[(2-aminophenyl)carbonylamino]-1-azanyl-1-oxidanylidene-hexan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration14 mg/mL
BufferpH: 6
Component:
ConcentrationName
20.0 mMSodium citrate
250.0 mMSodium chloride
0.001 %Lauryl Maltose Neopentyl Glycol (LMNG)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5n6l

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://pdbjlvh1.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