[English] 日本語
Yorodumi
- EMDB-50998: Cryo-EM structure of SbmA in the inward-facing-occluded conformat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50998
TitleCryo-EM structure of SbmA in the inward-facing-occluded conformation in lipid nanodiscs
Map data
Sample
  • Complex: Peptide antibiotic transporter SbmA in lipid nanodiscs
    • Protein or peptide: Peptide antibiotic transporter SbmA
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsPeptide antibiotic transporter SbmA / Peptide uptake permease (PUP) family / transmembrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


secondary active transmembrane transporter activity / microcin transmembrane transporter activity / microcin B17 transport / microcin transport / peptide transport / peptide transmembrane transporter activity / protein transport / response to antibiotic / protein homodimerization activity / ATP binding / plasma membrane
Similarity search - Function
SbmA/BacA-like / SbmA/BacA-like family / : / ABC transporter type 1, transmembrane domain superfamily
Similarity search - Domain/homology
Peptide antibiotic transporter SbmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsThangaratnarajah C / Ettema TW / Slotboom DJ
Funding support Netherlands, European Union, 4 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.018.003 Netherlands
Netherlands Organisation for Scientific Research (NWO)024.003.019 Netherlands
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
European Union (EU)847675European Union
CitationJournal: To Be Published
Title: Cryo-EM structure of the SbmA in the inward-facing closed conformation in lipid nanodiscs
Authors: Thangaratnarajah C / Ettema TW / Slotboom DJ
History
DepositionJul 12, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50998.png

Downloads & links

-
Map

FileDownload / File: emd_50998.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.)
1.02 Å/pix.
x 256 pix.
= 261.632 Å		1.02 Å/pix.
x 256 pix.
= 261.632 Å		1.02 Å/pix.
x 256 pix.
= 261.632 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.022 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-5.4136124 - 8.989001999999999
Average (Standard dev.)-0.00036203055 (±0.14407998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 261.632 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50998_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map.

Fileemd_50998_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 used during refinement and FSC...

Fileemd_50998_half_map_1.map
AnnotationHalf map 2 used during refinement and FSC gold-standard resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 used during refinement and FSC...

Fileemd_50998_half_map_2.map
AnnotationHalf map 1 used during refinement and FSC gold-standard resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Peptide antibiotic transporter SbmA in lipid nanodiscs

EntireName: Peptide antibiotic transporter SbmA in lipid nanodiscs
Components
  • Complex: Peptide antibiotic transporter SbmA in lipid nanodiscs
    • Protein or peptide: Peptide antibiotic transporter SbmA
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

-
Supramolecule #1: Peptide antibiotic transporter SbmA in lipid nanodiscs

SupramoleculeName: Peptide antibiotic transporter SbmA in lipid nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Peptide antibiotic transporter SbmA

MacromoleculeName: Peptide antibiotic transporter SbmA / type: protein_or_peptide / ID: 1 / Details: Protomer A / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.919664 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSI LGTALIIFVT WFLVEVGVAV NAWYAPFYDL IQTALSSPHK VTIEQFYREV GVFLGIALIA VVISVLNNFF V SHYVFRWR ...String:
MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSI LGTALIIFVT WFLVEVGVAV NAWYAPFYDL IQTALSSPHK VTIEQFYREV GVFLGIALIA VVISVLNNFF V SHYVFRWR TAMNEYYMAN WQQLRHIEGA AQRVQEDTMR FASTLENMGV SFINAIMTLI AFLPVLVTLS AHVPELPIIG HI PYGLVIA AIVWSLMGTG LLAVVGIKLP GLEFKNQRVE AAYRKELVYG EDDATRATPP TVRELFSAVR KNYFRLYFHY MYF NIARIL YLQVDNVFGL FLLFPSIVAG TITLGLMTQI TNVFGQVRGA FQYLINSWTT LVELMSIYKR LRSFEHELDG DKIQ EVTHT LSALEVLFQG PHHHHHHHHH H

UniProtKB: Peptide antibiotic transporter SbmA

-
Macromolecule #2: (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: 2 / Number of copies: 2 / 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

Concentration6.7 mg/mL
BufferpH: 5.5 / Details: 20 mM MES, pH 5.5, 120 mM NaCl, 0.05 % (w/v) DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 1933 / Average exposure time: 9.0 sec. / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 48924 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 804212
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated by the stochastic gradient decent (SGD) method.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 146295
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9g3g:
Cryo-EM structure of SbmA in the inward-facing-occluded conformation 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