[English] 日本語
Yorodumi
- EMDB-71294: Constituent EM map: Outer membrane and periplasmic portions of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71294
TitleConstituent EM map: Outer membrane and periplasmic portions of the lipopolysaccharide transport bridge from E coli
Map dataUnsharpened map
Sample
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB in complex with lipopolysaccharide
    • Complex: Outer membrane portion of lipopolysaccharide transporter with LptA
      • Protein or peptide: LptD
      • Protein or peptide: LptE
      • Protein or peptide: LptA
    • Complex: Inner membrane portion of lipopolysaccharide transporter
KeywordsComplex / Lipopolysaccharide / ABC / ATP binding cassette / transporter / bridge / intermembrane / LIPID TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 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
DepositionJun 17, 2025-
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_71294.png

Downloads & links

-
Map

FileDownload / File: emd_71294.map.gz / Format: CCP4 / Size: 824 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.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0582
Minimum - Maximum-0.094041586 - 0.20509928
Average (Standard dev.)-0.0001316246 (±0.0029640857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpened map

Fileemd_71294_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map

Fileemd_71294_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map

Fileemd_71294_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 in complex with lipopolysaccharide
Components
  • Complex: Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptA, LptC, LptF, LptG, and two molecules of LptB in complex with lipopolysaccharide
    • Complex: Outer membrane portion of lipopolysaccharide transporter with LptA
      • Protein or peptide: LptD
      • Protein or peptide: LptE
      • Protein or peptide: LptA
    • Complex: Inner membrane portion of lipopolysaccharide transporter

-
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 in complex with lipopolysaccharide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Outer membrane portion of lipopolysaccharide transporter with LptA

SupramoleculeName: Outer membrane portion of lipopolysaccharide transporter with LptA
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: Inner membrane portion of lipopolysaccharide transporter

SupramoleculeName: Inner membrane portion of lipopolysaccharide transporter
type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: LptD

MacromoleculeName: LptD / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRIPTLLA TMIATALYS Q QGLAADLA SQ CMLGVPS YDR PLVQGD TNDL PVTIN ADHAK GDYP DDAVFT GSV DIMQGNS RL QADEVQLH Q KEAPGQPEP VRTVDALGNV HYDDNQVIL K GPKGWANL NT KDTNVWE GDY QMVGRQ GRGK ADLMK ...String:
MKKRIPTLLA TMIATALYS Q QGLAADLA SQ CMLGVPS YDR PLVQGD TNDL PVTIN ADHAK GDYP DDAVFT GSV DIMQGNS RL QADEVQLH Q KEAPGQPEP VRTVDALGNV HYDDNQVIL K GPKGWANL NT KDTNVWE GDY QMVGRQ GRGK ADLMK QRGEN RYTI LDNGSF TSC LPGSDTW SV VGSEIIHD R EEQVAEIWN ARFKVGPVPI FYSPYLQLP V GDKRRSGF LI PNAKYTT TNY FEFYLP YYWN IAPNM DATIT PHYM HRRGNI MWE NEFRYLS QA GAGLMELD Y LPSDKVYED EHPNDDSSRR WLFYWNHSG V MDQVWRFN VD YTKVSDP SYF NDFDNK YGSS TDGYA TQKFS VGYA VQNFNA TVS TKQFQVF SE QNTSSYSA E PQLDVNYYQ NDVGPFDTRI YGQAVHFVN T RDDMPEAT RV HLEPTIN LPL SNNWGS INTE AKLLA THYQQ TNLD WYNSRN TTK LDESVNR VM PQFKVDGK M VFERDMEML APGYTQTLEP RAQYLYVPY R DQSDIYNY DS SLLQSDY SGL FRDRTY GGLD RIASA NQVTT GVTS RIYDDA AVE RFNISVG QI YYFTESRT G DDNITWEND DKTGSLVWAG DTYWRISER W GLRGGIQY DT RLDNVAT SNS SIEYRR DEDR LVQLN YRYAS PEYI QATLPK YYS TAEQYKN GI SQVGAVAS W PIADRWSIV GAYYYDTNAN KQADSMLGV Q YSSCCYAI RV GYERKLN GWD NDKQHA VYDN AIGFN IELRG LSSN YGLGTQ EML RSNILPY QN TL

-
Macromolecule #2: LptE

MacromoleculeName: LptE / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYLATLLLS LAVLITAGC G WHLRDTTQ VP STMKVMI LDS GDPNGP LSRA VRNQL RLNGV ELLD KETTRK DVP SLRLGKV SI AKDTASVF R NGQTAEYQM IMTVNATVLI PGRDIYPIS A KVFRSFFD NP QMALAKD NEQ DMIVKE MYDR AAEQL ...String:
MRYLATLLLS LAVLITAGC G WHLRDTTQ VP STMKVMI LDS GDPNGP LSRA VRNQL RLNGV ELLD KETTRK DVP SLRLGKV SI AKDTASVF R NGQTAEYQM IMTVNATVLI PGRDIYPIS A KVFRSFFD NP QMALAKD NEQ DMIVKE MYDR AAEQL IRKLP SIRA ADIRSD EEQ TSTTTDT PA TPARVSTT L GN

-
Macromolecule #3: LptA

MacromoleculeName: LptA / type: protein_or_peptide / ID: 3 / Details: LptA expressed as a fusion with LptC / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VTGDTDQPIH IESDQQSLDM QGNVVTFTGN VIVTQGTIKI NADKVVVTRP GGEQGKEVID GYGKPATFYQ MQDNGKPVEG HASQMHYELA KDFVVLTGNA YLQQVDSNIK GDKITYLVKE QKMQAFSDKG KRVTTVLVPS QLQDKNNKGQ TPAQKKGNLV PRGSHHHHHH H

-
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 KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 666000
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: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 157094
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