[English] 日本語
Yorodumi
- EMDB-12990: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12990
TitleCryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies
Map data
Sample
  • Complex: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
    • Protein or peptide: ProMacrobody 21,Maltodextrin-binding protein
    • Protein or peptide: ProMacrobody 51,Maltodextrin-binding protein
Function / homology
Function and homology information


lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / carbohydrate transmembrane transporter activity / : / cell outer membrane
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / LPS transport system D / Lipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / Pectin lyase fold/virulence factor / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltodextrin-binding protein / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria) / Methanosarcina mazei (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBotte M / Ni D / Schenck S / Zimmermann I / Chami M / Bocquet N / Egloff P / Bucher D / Trabuco M / Cheng RKY ...Botte M / Ni D / Schenck S / Zimmermann I / Chami M / Bocquet N / Egloff P / Bucher D / Trabuco M / Cheng RKY / Brunner JD / Seeger MA / Stahlberg H / Hennig M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Innosuisse25864.1 PFLS-LS Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation.
Authors: Mathieu Botte / Dongchun Ni / Stephan Schenck / Iwan Zimmermann / Mohamed Chami / Nicolas Bocquet / Pascal Egloff / Denis Bucher / Matilde Trabuco / Robert K Y Cheng / Janine D Brunner / ...Authors: Mathieu Botte / Dongchun Ni / Stephan Schenck / Iwan Zimmermann / Mohamed Chami / Nicolas Bocquet / Pascal Egloff / Denis Bucher / Matilde Trabuco / Robert K Y Cheng / Janine D Brunner / Markus A Seeger / Henning Stahlberg / Michael Hennig /
Abstract: Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram- ...Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram-negative bacteria. The last step of LPS insertion via the Lpt pathway is mediated by the LptD/E protein complex. Detailed insights into the architecture of LptDE transporter complexes have been derived from X-ray crystallography. However, no structure of a laterally open LptD transporter, a transient state that occurs during LPS release, is available to date. Here, we report a cryo-EM structure of a partially opened LptDE transporter in complex with rigid chaperones derived from nanobodies, at 3.4 Å resolution. In addition, a subset of particles allows to model a structure of a laterally fully opened LptDE complex. Our work offers insights into the mechanism of LPS insertion, provides a structural framework for the development of antibiotics targeting LptD and describes a highly rigid chaperone scaffold to enable structural biology of challenging protein targets.
History
DepositionMay 24, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateMay 11, 2022-
Current statusMay 11, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_12990.png

Downloads & links

-
Map

FileDownload / File: emd_12990.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.88308 Å
Density
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.7183622 - 3.965183
Average (Standard dev.)0.0027313337 (±0.048267312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacro...

EntireName: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies
Components
  • Complex: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
    • Protein or peptide: ProMacrobody 21,Maltodextrin-binding protein
    • Protein or peptide: ProMacrobody 51,Maltodextrin-binding protein

-
Supramolecule #1: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacro...

SupramoleculeName: Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)

-
Macromolecule #1: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)
Molecular weightTheoretical: 87.65693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARLFSLKPL VLSLGFCFGT HCAADTVAAE EADGRVAEGG AQGASESAQA SDLTLGSTCL FCSNESGSPE RTEAAVQGSG EASVPEDYT RIVADRMEGQ SKVKVRAEGS VIIERDGAVL NTDWADYDQS GDTVTVGDRF ALQQDGTLIR GETLTYNLDQ Q TGEAHNVR ...String:
MARLFSLKPL VLSLGFCFGT HCAADTVAAE EADGRVAEGG AQGASESAQA SDLTLGSTCL FCSNESGSPE RTEAAVQGSG EASVPEDYT RIVADRMEGQ SKVKVRAEGS VIIERDGAVL NTDWADYDQS GDTVTVGDRF ALQQDGTLIR GETLTYNLDQ Q TGEAHNVR METEQGGRRL QSVSRTAEML GEGRYKLTET QFNTCSAGDA GWYVKAASVE ADRGKGIGVA KHAAFVFGGV PL FYTPWAD FPLDGNRKSG LLVPSVSAGS DGVSLSVPYY FNLAPNFDAT FAPGIIGERG ATFDGQIRYL RPDYSGQTDL TWL PHDKKS GRNNRYQAKW QHRHDISDTL QAGVDFNQVS DSGYYRDFYG GEEIAGNVNL NRRVWLDYGG RAAGGSLNAG LSVQ KYQTL ANQSGYKDEP YAIMPRLSAD WHKNAGRAQI GVSAQFTRFS HDGRQDGSRL VVYPGIKWDF SNSWGYVRPK LGLHA TYYS LDSFGGKASR SVGRVLPVVN IDGGTTFERN TRLFGGGVVQ TIEPRLFYNY IPAKSQNDLP NFDSSESSFG YGQLFR ENL YYGNDRINAA NSLSTAVQSR ILDGATGEER FRAGIGQKFY FKDDAVMLDG SVGKNPRSRS DWVAFASGGI GGRFTLD SS IHYNQNDKRA EHYAVGAGYR PAPGKVLNAR YKYGRNEKIY LQADGSYFYD KLSQLDLSAQ WPLTRNLSAV VRYNYGFE A KKPIEMLAGA EYKSSCGCWG AGVYAQRYVT GENTYKNAVF FSLQLKDLSS VGRNPAGRMD VAVPGYIPAH SLSAGRNKR P

-
Macromolecule #2: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae (bacteria)
Molecular weightTheoretical: 18.499066 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNKIFLTAAA LVLGACGFHL KGADGISPPL TYRSWHIEGG QALQFPLETA LYQASGRVDD AAGAQMTLRI DSVSQNKETY TVTRAAVIN EYLLILTVEA QVLKRGEPVG KPMTVSVRRI LDYADNEILG KQEEEETLWA EMRQDVAEQI VRRLTFLKAE H HHHHH

-
Macromolecule #3: ProMacrobody 21,Maltodextrin-binding protein

MacromoleculeName: ProMacrobody 21,Maltodextrin-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina mazei (archaea)
Molecular weightTheoretical: 56.714457 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPSQVQLVES GGGLVQPGGS LRLSCAASGF PVKYEHMYWY RQAPGKEREW VAAINSAGNE THYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC NVKDIGWWAA YDYWGQGTQV TVPPLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK L EEKFPQVA ...String:
GPSQVQLVES GGGLVQPGGS LRLSCAASGF PVKYEHMYWY RQAPGKEREW VAAINSAGNE THYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC NVKDIGWWAA YDYWGQGTQV TVPPLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK L EEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LP NPPKTWE EIPALDKELK AKGKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKH MNADTD YSIAEAAFNK GETAMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENY LLTDE GLEAVNKDKP LGAVALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKD AQTP GSGGGSAWSH PQFEKGGGSG GGSGGSAWSH PQFEKA

-
Macromolecule #4: ProMacrobody 51,Maltodextrin-binding protein

MacromoleculeName: ProMacrobody 51,Maltodextrin-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina mazei (archaea)
Molecular weightTheoretical: 56.86159 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPSQVQLVES GGGSVQAGGS LRLSCAASGS ISSITYLGWF RQAPGKEREG VAALATYYGH TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAAYSGIWTP LGVWATYEYW GQGTQVTVPP LVIWINGDKG YNGLAEVGKK FEKDTGIKVT V EHPDKLEE ...String:
GPSQVQLVES GGGSVQAGGS LRLSCAASGS ISSITYLGWF RQAPGKEREG VAALATYYGH TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAAYSGIWTP LGVWATYEYW GQGTQVTVPP LVIWINGDKG YNGLAEVGKK FEKDTGIKVT V EHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IY NKDLLPN PPKTWEEIPA LDKELKAKGK SALMFNLQEP YFTWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVD LIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELAK EFLEN YLLTDEGLEA VNKDKPLGAV ALKSYEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTV DEAL KDAQTPGSGG GSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184206
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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://pdbjlvh1.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