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- PDB-9xdc: TamAB hybrid barrel state -

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Basic information

Entry
Database: PDB / ID: 9xdc
TitleTamAB hybrid barrel state
Components
  • Translocation and assembly module subunit TamA
  • Translocation and assembly module subunit TamB
KeywordsMEMBRANE PROTEIN / outer membrane / interaction / hybrid / TamAB / PROTEIN TRANSPORT / TamA / TamB / lipid transport / outer membrane insertion
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 str. K-12 substr. MG1655star (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsDong, C. / Zhang, Z. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The translocation and assembly module TamAB involves in outer membrane phospholipid transport and outer membrane protein insertion
Authors: Dong, C. / Zhang, Z. / Yang, B.
History
DepositionOct 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)201,7482
Polymers201,7482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Translocation and assembly module subunit TamA / Autotransporter assembly factor TamA


Mass: 64842.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia coli str. K-12 substr. MG1655star is not available, replaced by P0ADE4 temporarily.
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655star (bacteria)
Gene: tamA, yftM, ytfM, b4220, JW4179 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADE4
#2: 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: 136905.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia coli str. K-12 substr. MG1655star is not available, replaced by P39321 temporarily.
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655star (bacteria)
Gene: tamB, ytfN, ytfO, b4221, JW4180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39321
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: complex of the translocation and assembly module A and B
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110602 / Symmetry type: POINT
RefinementHighest resolution: 3.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026904
ELECTRON MICROSCOPYf_angle_d0.4699390
ELECTRON MICROSCOPYf_dihedral_angle_d5.411965
ELECTRON MICROSCOPYf_chiral_restr0.0441051
ELECTRON MICROSCOPYf_plane_restr0.0031236

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