[English] 日本語
Yorodumi
- EMDB-52200: Extracellular components BamHIJK of the Bacteroides thetaiotaomic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52200
TitleExtracellular components BamHIJK of the Bacteroides thetaiotaomicron BAM machinery
Map dataunsharpened map
Sample
  • Complex: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: DUF4270 domain-containing protein
    • Protein or peptide: DUF6242 domain-containing protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: DUF4827 domain-containing protein
  • Ligand: N-TRIDECANOIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
KeywordsLipoproteins / Outer membrane protein biogenesis / Beta-barrel assembly machinery / BAM / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Domain of unknown function DUF6242 / Domain of unknown function (DUF6242) / Protein of unknown function DUF4827 / Domain of unknown function (DUF4827) / Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
DUF4270 domain-containing protein / DUF4827 domain-containing protein / DUF6242 domain-containing protein / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsSilale A / van den Berg B
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM machinery
Authors: Silale A / van den Berg B
History
DepositionNov 27, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_52200.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Voxel sizeX=Y=Z: 0.74 Å
Density
Contour LevelBy AUTHOR: 0.0881
Minimum - Maximum-0.18528089 - 0.3909175
Average (Standard dev.)0.0010868156 (±0.01019823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Extracellular components BamGHIJ of the Bacteroides thetaiotaomic...

EntireName: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
Components
  • Complex: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
    • Protein or peptide: DUF4270 domain-containing protein
    • Protein or peptide: DUF6242 domain-containing protein
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase
    • Protein or peptide: DUF4827 domain-containing protein
  • Ligand: N-TRIDECANOIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

-
Supramolecule #1: Extracellular components BamGHIJ of the Bacteroides thetaiotaomic...

SupramoleculeName: Extracellular components BamGHIJ of the Bacteroides thetaiotaomicron BAM complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #1-#3
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 153 KDa

-
Macromolecule #1: DUF6242 domain-containing protein

MacromoleculeName: DUF6242 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 55.108051 KDa
SequenceString: MRIKFLSIIA SFFMVSFVIT SCLDNDNEVN YSPDATIRAF ELDTIGYGVN YKFTIDQVSR LIYNVDSLPV NADTIINSIL IKTLTTASG IVTMKDQNDQ DSIVNINDSI DLTKYVNATE KNNFLVLKVW APNMEVQNEY KVNIRMHTMV PDSLSWGKDP I ANNPVRNT ...String:
MRIKFLSIIA SFFMVSFVIT SCLDNDNEVN YSPDATIRAF ELDTIGYGVN YKFTIDQVSR LIYNVDSLPV NADTIINSIL IKTLTTASG IVTMKDQNDQ DSIVNINDSI DLTKYVNATE KNNFLVLKVW APNMEVQNEY KVNIRMHTMV PDSLSWGKDP I ANNPVRNT AEKQKVVTLG DKILLFAQNN EIYSTAIPAG SPTDRLNYGQ KWDKETTGKL PDGADVTSII RFVDKLYLLT KN KEVYNSN DGLTWTKDEV LNSDGVSVTN LITSFSDSDG SNHKKINGIA GIVEINGEKY FSFAEKDVTW EKDIDKLTVV PAE FPINNL SADVYATESG TLNAIVVGNT EDGLDNDTAT VVWASEDGKA WIPMEIPSNN NCPKLVDPSI IHYNDAFYIC GKET KDDAK GFQKFYTSPT LLVWKGVDRM FMLPGILPPV KLEGGVTQHP SLHESSFKGK EVNYTMVVDR NHYIWMVGGQ GIDKI WRGR VNKLGFLIQ

UniProtKB: DUF6242 domain-containing protein

-
Macromolecule #2: Peptidyl-prolyl cis-trans isomerase

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 21.884557 KDa
SequenceString: MSKKIYLFSL VLLALAFVSC SETEEVGKYD NWRARNEAFI DSLANVYATA SGRGGLERIE MLTAPGNYIY YKEMEPMTDH VVKAGNPKY TDYVKVYYKG TNILGEYFDG NFKGDNPVVD GKDPSEGDSP TTIFQVSGVI TGWGEVLQRM EVGDRWKVYI P WDYAYGSS ...String:
MSKKIYLFSL VLLALAFVSC SETEEVGKYD NWRARNEAFI DSLANVYATA SGRGGLERIE MLTAPGNYIY YKEMEPMTDH VVKAGNPKY TDYVKVYYKG TNILGEYFDG NFKGDNPVVD GKDPSEGDSP TTIFQVSGVI TGWGEVLQRM EVGDRWKVYI P WDYAYGSS GTTGILGYSA LVFDITLLDF ANTEAELK

UniProtKB: Peptidyl-prolyl cis-trans isomerase

-
Macromolecule #3: DUF4827 domain-containing protein

MacromoleculeName: DUF4827 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 24.712709 KDa
SequenceString: MKKLVFLFLS LLAAGGIFQA CDDSKTYAEM LEDEKNAVNK FIKDKGIRII SQDEFEKNDT VTNLERNEYV ALSDGVYMQI VDRGSAENK TDTFANNNEI CVRYIEEDIM TRDTTCFNVF LEEWGDANQL YTNPAVFRYV AEGSYVYGTF IQMDYYWASY Y QSTAVPAG ...String:
MKKLVFLFLS LLAAGGIFQA CDDSKTYAEM LEDEKNAVNK FIKDKGIRII SQDEFEKNDT VTNLERNEYV ALSDGVYMQI VDRGSAENK TDTFANNNEI CVRYIEEDIM TRDTTCFNVF LEEWGDANQL YTNPAVFRYV AEGSYVYGTF IQMDYYWASY Y QSTAVPAG WLLALPFVRN YAHVRLIVPS KVGHSSAQQY VNPYYYDIWT FSKALN

UniProtKB: DUF4827 domain-containing protein

-
Macromolecule #4: DUF4270 domain-containing protein

MacromoleculeName: DUF4270 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 58.264816 KDa
SequenceString: CDDNTGGLGL GMFPGNDQNI KGKLSTFDVT TESVKTGDIY AKTNIGYIGK FTDETFGTYQ AGFLAQLNCP DGLTFPEPYK EVTDASGNV ISATGRMVVD DKDPENKDVT FIKDGNQIIG NIRAVELYLW YDSYFGDSLT ACRLSVYELG GNGKETLNLD N AYYTDINP ...String:
CDDNTGGLGL GMFPGNDQNI KGKLSTFDVT TESVKTGDIY AKTNIGYIGK FTDETFGTYQ AGFLAQLNCP DGLTFPEPYK EVTDASGNV ISATGRMVVD DKDPENKDVT FIKDGNQIIG NIRAVELYLW YDSYFGDSLT ACRLSVYELG GNGKETLNLD N AYYTDINP EDFYDSQNIL GTKAYTAVDL SVKDSIRNLS TYVPSVHIAF KEDIATRVGG NILTAARKAK NADKEFNSQL FR EAFQGIY VKSDYGDGTV LYIDQPQMNV VYKCYATDSI TGKKLQKKDG SGKDSTYYSY RVFATTREVI QANQLKNDPE RID ALIKED KNTYLKSPAG IFTEATLPIS DIQNELTGDT LNAVKLTFTN YNQTGDKKFG MAIPSTVMLV RKKFQDSFFK DNKL SDGVS SYLTSHTSST NQYVFSNITK LVNACIAEKE EAKKNAGSSW DETKWLQENP DWNKVVLIPV LVTYDSSNTT TGQAN IIRI QHDLKPGYVR LKGGSLGKTN PDYKLKLEVI STDFGLTTKS N

UniProtKB: DUF4270 domain-containing protein

-
Macromolecule #5: N-TRIDECANOIC ACID

MacromoleculeName: N-TRIDECANOIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: TDA
Molecular weightTheoretical: 214.344 Da
Chemical component information

ChemComp-TDA:
N-TRIDECANOIC ACID

-
Macromolecule #6: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / type: ligand / ID: 6 / Number of copies: 1 / Formula: Z41
Molecular weightTheoretical: 568.911 Da
Chemical component information

ChemComp-Z41:
(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
10.0 mMHEPESHEPES
0.04 %DDMdodecyl maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 13558 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2266553
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48834
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement

-
Atomic model buiding 1

Initial model
PDB IDChain

7-f1

chain_id: I, source_name: AlphaFold, initial_model_type: in silico model

2-f1

chain_id: J, source_name: AlphaFold, initial_model_type: in silico model

9-f1

chain_id: H, source_name: AlphaFold, initial_model_type: in silico model

0-f1

chain_id: G, source_name: AlphaFold, initial_model_type: in silico model
DetailsAlphaFold2 models were docked using Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 58
Output model

PDB-9his:
Extracellular components BamHIJK of the Bacteroides thetaiotaomicron BAM machinery

+
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