[English] 日本語
Yorodumi
- EMDB-30923: CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30923
TitleCryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (MceA) complex
Map data
Sample
  • Complex: ManYZ trimer complex with Microcin E492 (MceA)
    • Protein or peptide: PTS system mannose-specific EIIC component
    • Protein or peptide: PTS system mannose-specific EIID component
    • Protein or peptide: Microcin E492
  • Ligand: alpha-D-mannopyranose
Function / homology
Function and homology information


mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / cytolysis / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / monoatomic ion transport / defense response to bacterium / membrane / plasma membrane
Similarity search - Function
Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile.
Similarity search - Domain/homology
PTS system mannose-specific EIIC component / PTS system mannose-specific EIID component / Microcin E492
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) / Klebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsWang JW / Zeng JW
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
National Natural Science Foundation of China (NSFC)31621092 China
CitationJournal: Cell Discov / Year: 2021
Title: Structure of the mannose phosphotransferase system (man-PTS) complexed with microcin E492, a pore-forming bacteriocin.
Authors: Kai Huang / Jianwei Zeng / Xueli Liu / Tianyu Jiang / Jiawei Wang /
History
DepositionJan 22, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateSep 1, 2021-
Current statusSep 1, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7dyr
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30923.png

Downloads & links

-
Map

FileDownload / File: emd_30923.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.05229045 - 0.13366638
Average (Standard dev.)4.3223616e-05 (±0.0016392269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 424.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.400424.400424.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0520.1340.000

-
Supplemental data

-
Sample components

-
Entire : ManYZ trimer complex with Microcin E492 (MceA)

EntireName: ManYZ trimer complex with Microcin E492 (MceA)
Components
  • Complex: ManYZ trimer complex with Microcin E492 (MceA)
    • Protein or peptide: PTS system mannose-specific EIIC component
    • Protein or peptide: PTS system mannose-specific EIID component
    • Protein or peptide: Microcin E492
  • Ligand: alpha-D-mannopyranose

-
Supramolecule #1: ManYZ trimer complex with Microcin E492 (MceA)

SupramoleculeName: ManYZ trimer complex with Microcin E492 (MceA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant strain: BL21
Molecular weightExperimental: 0.53 kDa/nm

-
Macromolecule #1: PTS system mannose-specific EIIC component

MacromoleculeName: PTS system mannose-specific EIIC component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 27.647621 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MEITTLQIVL VFIVACIAGM GSILDEFQFH RPLIACTLVG IVLGDMKTGI IIGGTLEMIA LGWMNIGAAV APDAALASII STILVIAGH QSIGAGIALA IPLAAAGQVL TIIVRTITVA FQHAADKAAD NGNLTAISWI HVSSLFLQAM RVAIPAVIVA L SVGTSEVQ ...String:
MEITTLQIVL VFIVACIAGM GSILDEFQFH RPLIACTLVG IVLGDMKTGI IIGGTLEMIA LGWMNIGAAV APDAALASII STILVIAGH QSIGAGIALA IPLAAAGQVL TIIVRTITVA FQHAADKAAD NGNLTAISWI HVSSLFLQAM RVAIPAVIVA L SVGTSEVQ NMLNAIPEVV TNGLNIAGGM IVVVGYAMVI NMMRAGYLMP FFYLGFVTAA FTNFNLVALG VIGTVMAVLY IQ LSPKYNR VAGAPAQAAG NNDLDNELD

-
Macromolecule #2: PTS system mannose-specific EIID component

MacromoleculeName: PTS system mannose-specific EIID component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 30.983373 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVDTTQTTTE KKLTQSDIRG VFLRSNLFQG SWNFERMQAL GFCFSMVPAI RRLYPENNEA RKQAIRRHLE FFNTQPFVAA PILGVTLAL EEQRANGAEI DDGAINGIKV GLMGPLAGVG DPIFWGTVRP VFAALGAGIA MSGSLLGPLL FFILFNLVRL A TRYYGVAY ...String:
MVDTTQTTTE KKLTQSDIRG VFLRSNLFQG SWNFERMQAL GFCFSMVPAI RRLYPENNEA RKQAIRRHLE FFNTQPFVAA PILGVTLAL EEQRANGAEI DDGAINGIKV GLMGPLAGVG DPIFWGTVRP VFAALGAGIA MSGSLLGPLL FFILFNLVRL A TRYYGVAY GYSKGIDIVK DMGGGFLQKL TEGASILGLF VMGALVNKWT HVNIPLVVSR ITDQTGKEHV TTVQTILDQL MP GLVPLLL TFACMWLLRK KVNPLWIIVG FFVIGIAGYA CGLLGL

-
Macromolecule #3: Microcin E492

MacromoleculeName: Microcin E492 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 7.887492 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GETDPNTQLL NDLGNNMAWG AALGAPGGLG SAALGAAGGA LQTVGQGLID HGPVNVPIPV LIGPSWNGSG SGYNSATSSS GSGS

-
Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92076
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