[English] 日本語
Yorodumi
- EMDB-76427: Consensus map: Low resolution structure of LPS transport bridge L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76427
TitleConsensus map: Low resolution structure of LPS transport bridge LptBFGCADE from Escherichia coli
Map dataUnsharpened map
Sample
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
    • Complex: Inner membrane portion of lipopolysaccharide transporter
      • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: Lipopolysaccharide export system permease protein LptF
      • Protein or peptide: Lipopolysaccharide export system permease protein LptG
    • Complex: Outer membrane portion of lipopolysaccharide transporter
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE
KeywordsComplex / Lipopolysaccharide / ABC / ATP binding cassette / transporter / bridge / intermembrane / LIPID TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsTaylor RJ / Pahil KS / Walsh Jr RM / Kahne DE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI149778 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081059 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI153358 United States
CitationJournal: To Be Published
Title: Structural basis for regulating lipopolysaccharide transmembrane transport
Authors: Taylor RJ / Pahil KS / Walsh Jr RM / Kahne DE
History
DepositionApr 5, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76427.png

Downloads & links

-
Map

FileDownload / File: emd_76427.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.234
Minimum - Maximum-0.13274606 - 0.5872395
Average (Standard dev.)0.0009772029 (±0.030750623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map

Fileemd_76427_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map

Fileemd_76427_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Intermembrane lipopolysaccharide transport bridge composed of Lpt...

EntireName: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
Components
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
    • Complex: Inner membrane portion of lipopolysaccharide transporter
      • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: Lipopolysaccharide export system permease protein LptF
      • Protein or peptide: Lipopolysaccharide export system permease protein LptG
    • Complex: Outer membrane portion of lipopolysaccharide transporter
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE

-
Supramolecule #1: Intermembrane lipopolysaccharide transport bridge composed of Lpt...

SupramoleculeName: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #2: Inner membrane portion of lipopolysaccharide transporter

SupramoleculeName: Inner membrane portion of lipopolysaccharide transporter
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #5-#6
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: Outer membrane portion of lipopolysaccharide transporter

SupramoleculeName: Outer membrane portion of lipopolysaccharide transporter
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Lipopolysaccharide export system ATP-binding protein LptB

MacromoleculeName: Lipopolysaccharide export system ATP-binding protein LptB
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDDDISLL PLHARARRGI GYLPQEASI FRRLSVYDNL MAVLQIRDDL SAEQREDRAN ELMEEFHIEH LRDSMGQSLS GGERRRVEIA RALAANPKFI L LDEPFAGV ...String:
MATLTAKNLA KAYKGRRVVE DVSLTVNSGE IVGLLGPNGA GKTTTFYMVV GIVPRDAGNI IIDDDDISLL PLHARARRGI GYLPQEASI FRRLSVYDNL MAVLQIRDDL SAEQREDRAN ELMEEFHIEH LRDSMGQSLS GGERRRVEIA RALAANPKFI L LDEPFAGV DPISVIDIKR IIEHLRDSGL GVLITDHNVR ETLAVCERAY IVSQGHLIAH GTPTEILQDE HVKRVYLGED FR L

-
Macromolecule #2: Lipopolysaccharide export system protein LptC,Lipopolysaccharide ...

MacromoleculeName: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKD KIPTWSVKAD KAKLTNDRML YLYGHVEVNA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS G LKMRGNLR ...String:
MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKD KIPTWSVKAD KAKLTNDRML YLYGHVEVNA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS G LKMRGNLR SKNAELIEKV RTSYEIQNKQ TQPLVPGGSG GGGSGGGGSG GGGSVTGDTD QPIHIESDQQ SLDMQGNVVT FT GNVIVTQ GTIKINADKV VVTRPGGEQG KEVIDGYGKP ATFYQMQDNG KPVEGHASQM HYELAKDFVV LTGNAYLQQV DSN IKGDKI TYLVKEQKMQ AFSDKGKRVT TVLVPSQLQD KNNKGQTPAQ KKGNLVPRGS HHHHHHH

-
Macromolecule #3: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG ...String:
MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG SFTSCLPGSD TWSVVGSEII HDREEQVAEI WNARFKVGPV PIFYSPYLQL PVGDKRRSGF LIPNAKYTTT NY FEFYLPY YWNIAPNMDA TITPHYMHRR GNIMWENEFR YLSQAGAGLM ELDYLPSDKV YEDEHPNDDS SRRWLFYWNH SGV MDQVWR FNVDYTKVSD PSYFNDFDNK YGSSTDGYAT QKFSVGYAVQ NFNATVSTKQ FQVFSEQNTS SYSAEPQLDV NYYQ NDVGP FDTRIYGQAV HFVNTRDDMP EATRVHLEPT INLPLSNNWG SINTEAKLLA THYQQTNLDW YNSRNTTKLD ESVNR VMPQ FKVDGKMVFE RDMEMLAPGY TQTLEPRAQY LYVPYRDQSD IYNYDSSLLQ SDYSGLFRDR TYGGLDRIAS ANQVTT GVT SRIYDDAAVE RFNISVGQIY YFTESRTGDD NITWENDDKT GSLVWAGDTY WRISERWGLR GGIQYDTRLD NVATSNS SI EYRRDEDRLV QLNYRYASPE YIQATLPKYY STAEQYKNGI SQVGAVASWP IADRWSIVGA YYYDTNANKQ ADSMLGVQ Y SSCCYAIRVG YERKLNGWDN DKQHAVYDNA IGFNIELRGL SSNYGLGTQE MLRSNILPYQ NTL

-
Macromolecule #4: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR ...String:
MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR SDEEQTSTTT DTPATPARVS TTLGN

-
Macromolecule #5: Lipopolysaccharide export system permease protein LptF

MacromoleculeName: Lipopolysaccharide export system permease protein LptF
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD ...String:
MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD FKDVFLAQIR PKGNARPSVV VADSGHLTQL RDGSQVVTLN QGTRFEGTAL LRDFRITDFQ DYQAIIGHQA VA LDPNDTD QMDMRTLWNT DTDRARAELN WRITLVFTVF MMALMVVPLS VVNPRQGRVL SMLPAMLLYL LFFLIQTSLK SNG GKGKLD PTLWMWTVNL IYLALAIVLN LWDTVPVRRL RASFSRKGAV

-
Macromolecule #6: Lipopolysaccharide export system permease protein LptG

MacromoleculeName: Lipopolysaccharide export system permease protein LptG
type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR MQVALSVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQA MYGGSLLSTQ QGLWAKDGNN F VYIERVKG ...String:
MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR MQVALSVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQA MYGGSLLSTQ QGLWAKDGNN F VYIERVKG DEELGGISIY AFNENRRLQS VRYAATAKFD PEHKVWRLSQ VDESDLTNPK QITGSQTVSG TWKTNLTPDK LG VVALDPD ALSISGLHNY VKYLKSSGQD AGRYQLNMWS KIFQPLSVAV MMLMALSFIF GPLRSVPMGV RVVTGISFGF VFY VLDQIF GPLTLVYGIP PIIGALLPSA SFFLISLWLL MRKS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3Tris pH 8
150.0 mMNaClSodium Chloride
0.02 %C56H92O25glyco-diosgenin
1.0 %C3H8O3glycerol
1.0 %C2H6OSDMSO
1.0 %C2H6O2ethylene glycol

Details: 20mM Tris HCl, 150mM NaCl, 1% glycerol, 1% DMSO, 1% ethylene glycol, 0.02% GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse as determined by SEC.

-
Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm

+
Image processing

Particle selectionNumber selected: 59141
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Ab initio model generated based on the data using cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24008
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - 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