[English] 日本語
Yorodumi
- PDB-23sp: TamA complex with TamB DUF490 in lipid nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 23sp
TitleTamA complex with TamB DUF490 in lipid nanodisc
Components
  • Translocation and assembly module subunit TamA
  • Translocation and assembly module subunit TamB
KeywordsMEMBRANE PROTEIN / beta barrel / TAM / complex / OMP
Function / homology
Function and homology information


TAM protein secretion complex / protein localization to outer membrane / protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
Translocation and assembly module TamB / TamB C-terminal domain / TamA, POTRA domain 1 / POTRA domain TamA domain 1 / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Translocation and assembly module subunit TamA / Translocation and assembly module subunit TamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsAdamson, L.S.R. / Doyle, M.T. / Grosas, A.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP260100880 Australia
Citation
Journal: bioRxiv / Year: 2026
Title: Mechanism of phospholipid transport to the bacterial outer membrane by TAM.
Authors: Alanah G Eisenhuth / Lachlan S R Adamson / Catherine Zhang / Ghaeath S K Abbas / Rachel A North / Denisse L Leyton / Harris D Bernstein / Simon H J Brown / Alastair G Stewart / Constance B ...Authors: Alanah G Eisenhuth / Lachlan S R Adamson / Catherine Zhang / Ghaeath S K Abbas / Rachel A North / Denisse L Leyton / Harris D Bernstein / Simon H J Brown / Alastair G Stewart / Constance B Bailey / Anthony S Don / Aidan B Grosas / Matthew Thomas Doyle /
Abstract: Gram-negative bacteria transport phospholipids from the inner membrane (IM) to the outer membrane (OM) via poorly understood processes. These processes are essential for cell growth and the ...Gram-negative bacteria transport phospholipids from the inner membrane (IM) to the outer membrane (OM) via poorly understood processes. These processes are essential for cell growth and the establishment of an antibiotic-resistant barrier. Here, we conducted single-particle cryo-electron microscopy, functional assays, and lipidomics to investigate the role of the "translocation and assembly module" (TAM) in lipid transport. We found that the OM-embedded subunit TamA anchors the IM-embedded bridge-like subunit TamB to the OM by forming a functional stable hybrid-barrel structure with the highly conserved C-terminal domain of unknown function 490 (DUF490). Using disulfide-tethering experiments we found that a highly conserved amphipathic helix within TamB DUF490 is important for TAM to function in OM maintenance. We also found that TamB DUF490 forms a β-taco channel containing lipid-like densities and that the lipophilic property of the channel is important for TAM to maintain the levels of cardiolipin in the OM. Not only do our data support a novel model in which TAM acts to direct specific lipid classes into the OM, but it also supports the notion that TamB is a bacterial evolutionary prototype of a structurally homologous superfamily of eukaryotic bridge-like lipid transfer proteins.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionFeb 16, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Translocation and assembly module subunit TamB
A: Translocation and assembly module subunit TamA


Theoretical massNumber of molelcules
Total (without water)112,9652
Polymers112,9652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, cross-linking, In vivo disulfide crosslinking experiments on E. coli.
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Translocation and assembly module subunit TamB / Autotransporter assembly factor TamB / Intermembrane phospholipid transporter TamB / Phospholipid ...Autotransporter assembly factor TamB / Intermembrane phospholipid transporter TamB / Phospholipid transport protein TamB


Mass: 48738.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 837-1259 of E. coli Translocation and Assembly Module subunit B.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tamB, ytfN, ytfO, b4221, JW4180 / Production host: Escherichia coli (E. coli) / References: UniProt: P39321
#2: Protein Translocation and assembly module subunit TamA / Autotransporter assembly factor TamA


Mass: 64225.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E. coli Translocation and Assembly Module subunit A.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tamA, yftM, ytfM, b4220, JW4179 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADE4
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Complex of translocation and assembly module subunit A (TamA) with translocation and assembly module subuni B DUF490 (TamB DUF490).
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1128 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 50 mM Tris pH 8 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTrisC4H11NO31
SpecimenConc.: 2.46 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was prepared in MSP1D1 nanodiscs with E. coli polar lipid extract.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3 uL sample applied for blotting. Wait time of 60s, blot time of 3s with a blot force of 9.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARC4.7.0CTF correction
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103937 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 103.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00657791
ELECTRON MICROSCOPYf_angle_d1.070310578
ELECTRON MICROSCOPYf_chiral_restr0.06021165
ELECTRON MICROSCOPYf_plane_restr0.01051390
ELECTRON MICROSCOPYf_dihedral_angle_d13.49132865

+
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