[English] 日本語
Yorodumi
- PDB-38ol: LPT translocon complex from Flavobacter johnsoniae built in compo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 38ol
TitleLPT translocon complex from Flavobacter johnsoniae built in composite volume
Components
  • (Hypothetical ...) x 4
  • DUF5683 domain-containing protein
  • Organic solvent tolerance protein OstA-like protein
  • OstA family protein
  • Outer membrane protein beta-barrel domain-containing protein
  • Porin
KeywordsMEMBRANE PROTEIN / LPS transport SLP transport outer membrane protein complex
Function / homology
Function and homology information


glycolipid transfer activity / transporter complex / outer membrane / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / outer membrane-bounded periplasmic space
Similarity search - Function
Putative porin-10 / Domain of unknown function DUF5683 / Protein of unknown function DUF6452 / LPS-assembly protein LptD, central domain / Protein of unknown function DUF6048 / OstA-like protein / Putative porin / Family of unknown function (DUF5683) / Domain of unknown function (DUF6048) / LptD protein ...Putative porin-10 / Domain of unknown function DUF5683 / Protein of unknown function DUF6452 / LPS-assembly protein LptD, central domain / Protein of unknown function DUF6048 / OstA-like protein / Putative porin / Family of unknown function (DUF5683) / Domain of unknown function (DUF6048) / LptD protein / Family of unknown function (DUF6452) / SbsA, Ig-like domain / : / Bacterial Ig-like domain / : / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
alpha-D-galactopyranose / Organic solvent tolerance protein OstA-like protein / OstA family protein / Hypothetical lipoprotein / Hypothetical lipoprotein / Outer membrane protein beta-barrel domain-containing protein / Porin / Hypothetical lipoprotein / Hypothetical lipoprotein / DUF5683 domain-containing protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLea, S.M. / Berks, B.C.
Funding support United States, European Union, 3items
OrganizationGrant numberCountry
Other private United States
European Research Council (ERC)101201241European Union
European Research Council (ERC)833713European Union
CitationJournal: To Be Published
Title: An expanded LPS translocon mediates surface lipoprotein export in the Bacteroidota
Authors: Liu, X. / Orenday Tapia, L. / Bryant, O.J. / Lea, S.M. / Berks, B.C.
History
DepositionSep 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: Hypothetical lipoprotein
A: OstA family protein
N: Porin
S2: Hypothetical lipoprotein
Q: Outer membrane protein beta-barrel domain-containing protein
R: Hypothetical lipoprotein
T: DUF5683 domain-containing protein
S1: Hypothetical lipoprotein
D: Organic solvent tolerance protein OstA-like protein
E: Hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,53322
Polymers474,79010
Non-polymers3,74312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Hypothetical ... , 4 types, 5 molecules PS2S1RE

#1: Protein Hypothetical lipoprotein


Mass: 65414.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FM71
#4: Protein Hypothetical lipoprotein


Mass: 36815.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FGY9
#6: Protein Hypothetical lipoprotein


Mass: 20104.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FGZ0
#9: Protein Hypothetical lipoprotein


Mass: 19251.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FIT9

-
Protein , 5 types, 5 molecules ANQTD

#2: Protein OstA family protein


Mass: 62401.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FGP3
#3: Protein Porin


Mass: 76868.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FIK3
#5: Protein Outer membrane protein beta-barrel domain-containing protein


Mass: 31259.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FGZ4
#7: Protein DUF5683 domain-containing protein


Mass: 21526.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FNH9
#8: Protein Organic solvent tolerance protein OstA-like protein


Mass: 104330.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
References: UniProt: A5FB33

-
Sugars , 3 types, 12 molecules

#10: Polysaccharide
alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 502.421 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpAa1-2[LRhapa1-4]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a2122A-1a_1-5][a2211m-1a_1-5]/1-2-3/a2-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(2+1)][a-D-GlcpA]{}[(4+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#11: Polysaccharide alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-4DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5][a2211m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(4+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#12: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: LPT complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Data were collected at both 200kV and 300kV on two different Titan Krios and an Arctica
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Details: Data were collected on three microscopes Titan Krios / Gatan K3 BioQuantum Titan Krios / Falcon 4i Arctica / Gatan K3 BioQuantum

-
Processing

EM software
IDNameVersionCategory
1SIMPLEparticle selection
2PHENIX2.2_6143model refinement
13cryoSPARC3D reconstruction
Image processingDetails: Data were combined from two different Gatan K3 Bioquantum detectors and a Falcon 4i
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218874
Details: The volume is a composite volume - the numbers of particles used for the different components varied from 218,874 to 70,401 particles Resolution varied from 2.9 to 3.5
Symmetry type: POINT

+
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