[English] 日本語
Yorodumi
- EMDB-25713: CryoEM structure of the YejM/LapB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25713
TitleCryoEM structure of the YejM/LapB complex
Map datasharpened map with a B factor of -216 A2
Sample
  • Complex: complex of YejM and YciM
    • Protein or peptide: Lipopolysaccharide assembly protein B
    • Protein or peptide: Inner membrane protein YejM
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
KeywordsYejM / YciM / regulation / lipopolysaccharide synthesis / LpxC / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / lipopolysaccharide metabolic process / regulation of lipid biosynthetic process / membrane => GO:0016020 / iron ion binding / plasma membrane
Similarity search - Function
Lipopolysaccharide assembly protein B / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / : / Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily ...Lipopolysaccharide assembly protein B / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / : / Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Inner membrane protein YejM / Lipopolysaccharide assembly protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMi W / Shu S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli.
Authors: Sheng Shu / Wei Mi /
Abstract: Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH- ...Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels.
History
DepositionDec 13, 2021-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25713.png

Downloads & links

-
Map

FileDownload / File: emd_25713.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map with a B factor of -216 A2
Voxel sizeX=Y=Z: 1.346 Å
Density
Contour LevelBy AUTHOR: 0.214
Minimum - Maximum-2.5662167 - 3.411676
Average (Standard dev.)0.007598466 (±0.059201136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 258.432 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_25713_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: original 3D reconstruction without sharpening

Fileemd_25713_additional_1.map
Annotationoriginal 3D reconstruction without sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25713_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25713_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of YejM and YciM

EntireName: complex of YejM and YciM
Components
  • Complex: complex of YejM and YciM
    • Protein or peptide: Lipopolysaccharide assembly protein B
    • Protein or peptide: Inner membrane protein YejM
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE

-
Supramolecule #1: complex of YejM and YciM

SupramoleculeName: complex of YejM and YciM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 225.556 kDa/nm

-
Macromolecule #1: Lipopolysaccharide assembly protein B

MacromoleculeName: Lipopolysaccharide assembly protein B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.546953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLELLFLLLP VAAAYGWYMG RRSAQQNKQD EANRLSRDYV AGVNFLLSNQ QDKAVDLFLD MLKEDTGTVE AHLTLGNLFR SRGEVDRAI RIHQTLMESA SLTYEQRLLA IQQLGRDYMA AGLYDRAEDM FNQLTDETDF RIGALQQLLQ IYQATSEWQK A IDVAERLV ...String:
MLELLFLLLP VAAAYGWYMG RRSAQQNKQD EANRLSRDYV AGVNFLLSNQ QDKAVDLFLD MLKEDTGTVE AHLTLGNLFR SRGEVDRAI RIHQTLMESA SLTYEQRLLA IQQLGRDYMA AGLYDRAEDM FNQLTDETDF RIGALQQLLQ IYQATSEWQK A IDVAERLV KLGKDKQRVE IAHFYCELAL QHMASDDLDR AMTLLKKGAA ADKNSARVSI MMGRVFMAKG EYAKAVESLQ RV ISQDREL VSETLEMLQT CYQQLGKTAE WAEFLQRAVE ENTGADAELM LADIIEARDG SEAAQVYITR QLQRHPTMRV FHK LMDYHL NEAEEGRAKE SLMVLRDMVG EKVRSKPRYR CQKCGFTAYT LYWHCPSCRA WSTIKPIRGL DGLEHHHHHH

UniProtKB: Lipopolysaccharide assembly protein B

-
Macromolecule #2: Inner membrane protein YejM

MacromoleculeName: Inner membrane protein YejM / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 67.36468 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVTHRQRYRE KVSQMVSWGH WFALFNILLS LVIGSRYLFI ADWPTTLAGR IYSYVSIIGH FSFLVFATYL LILFPLTFIV GSQRLMRFL SVILATAGMT LLLIDSEVFT RFHLHLNPIV WQLVINPDEN EMARDWQLMF ISVPVILLLE LVFATWSWQK L RSLTRRRR ...String:
MVTHRQRYRE KVSQMVSWGH WFALFNILLS LVIGSRYLFI ADWPTTLAGR IYSYVSIIGH FSFLVFATYL LILFPLTFIV GSQRLMRFL SVILATAGMT LLLIDSEVFT RFHLHLNPIV WQLVINPDEN EMARDWQLMF ISVPVILLLE LVFATWSWQK L RSLTRRRR FARPLAAFLF IAFIASHVVY IWADANFYRP ITMQRANLPL SYPMTARRFL EKHGLLDAQE YQRRLIEQGN PD AVSVQYP LSELRYRDMG TGQNVLLITV DGLNYSRFEK QMPALAGFAE QNISFTRHMS SGNTTDNGIF GLFYGISPSY MDG ILSTRT PAALITALNQ QGYQLGLFSS DGFTSPLYRQ ALLSDFSMPS VRTQSDEQTA TQWINWLGRY AQEDNRWFSW VSFN GTNID DSNQQAFARK YSRAAGNVDD QINRVLNALR DSGKLDNTVV IITAGRGIPL SEEEETFDWS HGHLQVPLVI HWPGT PAQR INALTDHTDL MTTLMQRLLH VSTPASEYSQ GQDLFNPQRR HYWVTAADND TLAITTPKKT LVLNNNGKYR TYNLRG ERV KDEKPQLSLL LQVLTDEKRF IAN

UniProtKB: Inner membrane protein YejM

-
Macromolecule #3: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 3 / Number of copies: 1 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

-
Macromolecule #4: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 4 / Number of copies: 1 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 7.8
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 8.84 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 1181379
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7t6d:
CryoEM structure of the YejM/LapB complex

+
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