[English] 日本語
Yorodumi
- EMDB-51037: CryoEM structure of the proton-dependent antibacterial peptide tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51037
TitleCryoEM structure of the proton-dependent antibacterial peptide transporter SbmA in complex with FabS11-1 in lipid nanodiscs at pH 5.5, inward-closed state
Map dataUnsharpened consensus map
Sample
  • Complex: A dimer of SbmA bound to a single Fab S11-1
    • Complex: SbmA dimer
      • Protein or peptide: Peptide antibiotic transporter SbmA
    • Complex: Single FabS11-1
      • Protein or peptide: 11-1 FabH
      • Protein or peptide: 11-1 FabL
KeywordsSLiPT / antibacterial peptide / microcin / 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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsGhilarov D / Beis K
Funding support United Kingdom, European Union, 4 items
OrganizationGrant numberCountry
Wellcome Trust221868/Z/20/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H01778X/1 United Kingdom
European Regional Development FundTEAM/2016-3/23European Union
CitationJournal: To Be Published
Title: Structure and mechanism of SLiPT transporters
Authors: Ettema TW / Thangaratnarajah C / Inoue-Inaba S
History
DepositionJul 15, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51037.png

Downloads & links

-
Map

FileDownload / File: emd_51037.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3285502 - 0.5626111
Average (Standard dev.)0.00018243877 (±0.011576152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half-map A

Fileemd_51037_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B

Fileemd_51037_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A dimer of SbmA bound to a single Fab S11-1

EntireName: A dimer of SbmA bound to a single Fab S11-1
Components
  • Complex: A dimer of SbmA bound to a single Fab S11-1
    • Complex: SbmA dimer
      • Protein or peptide: Peptide antibiotic transporter SbmA
    • Complex: Single FabS11-1
      • Protein or peptide: 11-1 FabH
      • Protein or peptide: 11-1 FabL

-
Supramolecule #1: A dimer of SbmA bound to a single Fab S11-1

SupramoleculeName: A dimer of SbmA bound to a single Fab S11-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: SbmA dimer

SupramoleculeName: SbmA dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: Single FabS11-1

SupramoleculeName: Single FabS11-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Peptide antibiotic transporter SbmA

MacromoleculeName: Peptide antibiotic transporter SbmA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 46.496039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVGL FALFWFIYSP HRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV S HYVFRWRT ...String:
MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVGL FALFWFIYSP HRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV S HYVFRWRT AMNEYYMANW QQLRHIEGAA QRVQEDTMRF ASTLENMGVS FINAIMTLIA FLPVLVTLSA HVPELPIIGH IP YGLVIAA IVWSLMGTGL LAVVGIKLPG LEFKNQRVEA AYRKELVYGE DDATRATPPT VRELFSAVRK NYFRLYFHYM YFN IARILY LQVDNVFGLF LLFPSIVAGT ITLGLMTQIT NVFGQVRGAF QYLINSWTTL VELMSIYKRL RSFEHELDGD KIQE VTHTL S

UniProtKB: Peptide antibiotic transporter SbmA

-
Macromolecule #2: 11-1 FabH

MacromoleculeName: 11-1 FabH / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.932156 KDa
SequenceString: LKLLDSGAEL VKPGASVKLS CTASGFNIKD TYMYWVKQRP DQGLEWIGRI DPANGNSKYD PKFQGKATIT ADTSSNTAYL QVSSLTSED TAVYYCARWL VRGRRGTMDY WGQGTSVTVS SAKTTAPSVY PLAPVCGDTT GSSVTLGCLV KGYFPEPVTL T WNSGSLSS ...String:
LKLLDSGAEL VKPGASVKLS CTASGFNIKD TYMYWVKQRP DQGLEWIGRI DPANGNSKYD PKFQGKATIT ADTSSNTAYL QVSSLTSED TAVYYCARWL VRGRRGTMDY WGQGTSVTVS SAKTTAPSVY PLAPVCGDTT GSSVTLGCLV KGYFPEPVTL T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PRGPTIKPCP PCKCP

-
Macromolecule #3: 11-1 FabL

MacromoleculeName: 11-1 FabL / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.318711 KDa
SequenceString: DIVMTQSPAI LSASPGEKVT MTCRASSSVS YMHWYQQKPG SSPKPWIYAT SNLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPRTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIVMTQSPAI LSASPGEKVT MTCRASSSVS YMHWYQQKPG SSPKPWIYAT SNLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPRTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 5.5 / Component - Concentration: 20.0 mM / Component - Name: MES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsSbmA-Fab complex in lipid nanodiscs

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50775
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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