[English] 日本語
Yorodumi
- EMDB-13268: Streptococcus pneumoniae choline importer LicB in lipid nanodiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13268
TitleStreptococcus pneumoniae choline importer LicB in lipid nanodiscs
Map data
Sample
  • Complex: Choline importer in nanodiscs bound to nanobody
    • Protein or peptide: Nanobody
    • Protein or peptide: LicB protein
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsImporter / Choline / nanodisc / Nanobody / TRANSPORT PROTEIN
Function / homologyEamA domain / EamA-like transporter family / membrane / LicB protein
Function and homology information
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsPerez C / Baerland N
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_170607 Switzerland
Citation
Journal: Sci Adv / Year: 2022
Title: Mechanistic basis of choline import involved in teichoic acids and lipopolysaccharide modification.
Authors: Natalie Bärland / Anne-Stéphanie Rueff / Gonzalo Cebrero / Cedric A J Hutter / Markus A Seeger / Jan-Willem Veening / Camilo Perez /
Abstract: Phosphocholine molecules decorating bacterial cell wall teichoic acids and outer-membrane lipopolysaccharide have fundamental roles in adhesion to host cells, immune evasion, and persistence. ...Phosphocholine molecules decorating bacterial cell wall teichoic acids and outer-membrane lipopolysaccharide have fundamental roles in adhesion to host cells, immune evasion, and persistence. Bacteria carrying the operon that performs phosphocholine decoration synthesize phosphocholine after uptake of the choline precursor by LicB, a conserved transporter among divergent species. is a prominent pathogen where phosphocholine decoration plays a fundamental role in virulence. Here, we present cryo-electron microscopy and crystal structures of LicB, revealing distinct conformational states and describing architectural and mechanistic elements essential to choline import. Together with in vitro and in vivo functional characterization, we found that LicB displays proton-coupled import activity and promiscuous selectivity involved in adaptation to choline deprivation conditions, and describe LicB inhibition by synthetic nanobodies (sybodies). Our results provide previously unknown insights into the molecular mechanism of a key transporter involved in bacterial pathogenesis and establish a basis for inhibition of the phosphocholine modification pathway across bacterial phyla.
#1: Journal: Biorxiv / Year: 2021
Title: Mechanistic basis of choline import involved in teichoic acids and lipopolysaccharide modification
Authors: Barland N / Rueff AS / Cebrero G / Hutter CA / Seeger MA / Veening JW / Perez C
History
DepositionJul 29, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.135
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.135
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7paf
  • Surface level: 0.135
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13268.png

Downloads & links

-
Map

FileDownload / File: emd_13268.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 384 pix.
= 337.152 Å		0.88 Å/pix.
x 384 pix.
= 337.152 Å		0.88 Å/pix.
x 384 pix.
= 337.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135 / Movie #1: 0.135
Minimum - Maximum-0.6427229 - 0.95486265
Average (Standard dev.)-0.000046419427 (±0.01275228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 337.152 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8780.8780.878
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z337.152337.152337.152
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.6430.955-0.000

-
Supplemental data

-
Mask #1

Fileemd_13268_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Choline importer in nanodiscs bound to nanobody

EntireName: Choline importer in nanodiscs bound to nanobody
Components
  • Complex: Choline importer in nanodiscs bound to nanobody
    • Protein or peptide: Nanobody
    • Protein or peptide: LicB protein
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

-
Supramolecule #1: Choline importer in nanodiscs bound to nanobody

SupramoleculeName: Choline importer in nanodiscs bound to nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Streptococcus pneumoniae TIGR4 (bacteria)
Molecular weightTheoretical: 260 KDa

-
Macromolecule #1: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.802365 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
GSSSQVQLVE SGGGSVQAGG SLRLSCAASG TIHAIGYLGW FRQAPGKERE GVAALTTYDG WTYYADSVKG RFTVSLDNAK NTVYLQMNS LKPEDTALYY CAAADDGWMF PLYHNHYEYW GQGTQVTVSA GRAGEQKLIS EEDLNSAVDH HHHHH

-
Macromolecule #2: LicB protein

MacromoleculeName: LicB protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae TIGR4 (bacteria) / Strain: ATCC BAA-334 / TIGR4
Molecular weightTheoretical: 31.647631 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKSKNGVPFG LLSGIFWGLG LTVSAYIFSI FTDLSPFVVA ATHDFLSIFI LLAFLLVKEG KVRLSIFLNI RNVSVIIGAL LAGPIGMQA NLYAVKYIGS SLASSVSAIY PAISVLLAFF FLKHKISKNT VFGIVLIIGG IIAQTYKVEQ VNSFYIGILC A LVCAIAWG ...String:
MKSKNGVPFG LLSGIFWGLG LTVSAYIFSI FTDLSPFVVA ATHDFLSIFI LLAFLLVKEG KVRLSIFLNI RNVSVIIGAL LAGPIGMQA NLYAVKYIGS SLASSVSAIY PAISVLLAFF FLKHKISKNT VFGIVLIIGG IIAQTYKVEQ VNSFYIGILC A LVCAIAWG SESVLSSFAM ESELSEIEAL LIRQVTSFLS YLVIVLFSHQ SFTAVANGQL LGLMIVFAAF DMISYLAYYI AI NRLQPAK ATGLNVSYVV WTVLFAVVFL GAPLDMLTIM TSLVVIAGVY IIIKE

UniProtKB: LicB protein

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

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 3 / Number of copies: 1 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.0 µm

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.2.0) / Number images used: 78649
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v3.2.0)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. v3.2.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. v3.2.0)

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7paf:
Streptococcus pneumoniae choline importer LicB in lipid nanodiscs

+
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