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- PDB-9xdd: TamAB in non-hybrid barrel state -

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Basic information

Entry
Database: PDB / ID: 9xdd
TitleTamAB in non-hybrid barrel state
Components
  • Translocation and assembly module subunit TamA
  • Translocation and assembly module subunit TamB
KeywordsMEMBRANE PROTEIN / outer membrane / interaction / non-hybrid / TamAB / PROTEIN TRANSPORT / TamA / TamB / phospholipid transport
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. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsDong, C. / Zhang, Z. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of outer membrane biogenesis by the TamAB translocase.
Authors: Biao Yang / Ruixin Fan / Mariana Bunoro Batista / Yatian Chen / Xiaofeng Duan / Rong Wang / Danyang Li / Phillip J Stansfeld / Zhengyu Zhang / Changjiang Dong /
Abstract: The outer membrane is vital for Gram-negative bacteria, playing crucial roles in colonization, pathogenesis and drug resistance. The translocation and assembly module A and B (TamAB) nanomachinery ...The outer membrane is vital for Gram-negative bacteria, playing crucial roles in colonization, pathogenesis and drug resistance. The translocation and assembly module A and B (TamAB) nanomachinery has been reported to be involved in transport of phospholipids from the inner membrane to the outer membrane, as well as insertion of critical outer membrane proteins. However, the underlying mechanisms remain poorly understood. Here we report cryogenic electron microscopy structures of TamAB in two conformations at resolutions of 3.69 and 3.82 Å. We reveal a hybrid barrel structure formed between the first β-strand of the TamA barrel and the last β-strand of the TamB C-terminal domain, which is folded inside the β-barrel. By integrating structural analysis with functional data, biochemical assays, and molecular dynamics simulations, we identify key residues involved in TamAB interactions and characterize the mechanisms of anterograde phospholipid transport within the continuously beta-helical hydrophobic cavity of TamB. Through disulfide bond crosslinking and functional assays, we reveal that TamA crosslinks with both TamB and Ag43. Additionally, we confirm that the two cryo-EM conformational states of TamAB exist in vivo. While BAM overexpression can compensate for TamAB deletion in Ag43 insertion, it does not rescue phospholipid transport. Given that TamA and TamB orthologs are widely distributed in among bacterial and eukaryotic organisms, our findings have broad implications in cell envelope biogenesis and offer potential avenues for therapeutic development through inhibition.
History
DepositionOct 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: 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. MG1655 (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: MSLWKKISLGVVIVILLLLGSVAFLVGTTSGLHLVFKAADRWVPGLDIGKVTGGWRDLTLSDVRYEQPGVAVKAGNLHLA VGLECLWNSSVCINDLALKDIQVNIDSKKMPPSEQVEEEEDSGPLDLSTPYPITLTRVALDNVNIKIDDTTVSVMDFTSG ...Details: MSLWKKISLGVVIVILLLLGSVAFLVGTTSGLHLVFKAADRWVPGLDIGKVTGGWRDLTLSDVRYEQPGVAVKAGNLHLA VGLECLWNSSVCINDLALKDIQVNIDSKKMPPSEQVEEEEDSGPLDLSTPYPITLTRVALDNVNIKIDDTTVSVMDFTSG LNWQEKTLTLKPTSLKGLLIALPKVAEVAQEEVVEPKIENPQPDEKPLGETLKDLFSRPVLPEMTDVHLPLNLNIEEFKG EQLRVTGDTDITVSTMLLKVSSIDGNTKLDALDIDSSQGIVNASGTAQLSDNWPVDITLNSTLNVEPLKGEKVKLKMGGA LREQLEIGVNLSGPVDMDLRAQTRLAEAGLPLNVEVNSKQLYWPFTGEKQYQADDLKLKLTGKMTDYTLSMRTAVKGQEI PPATITLDAKGNEQQVNLDKLTVAALEGKTELKALLDWQQAISWRGELTLNGINTAKEFPDWPSKLNGLIKTRGSLYGGT WQMDVPELKLTGNVKQNKVNVDGTLKGNSYMQWMIPGLHLELGPNSAEVKGELGVKDLNLDATINAPGLDNALPGLGGTA KGLVKVRGTVEAPQLLADITARGLRWQELSVAQVRVEGDIKSTDQIAGKLDVRVEQISQPDVNINLVTLNAKGSEKQHEL QLRIQGEPVSGQLNLAGSFDRKEERWKGTLSNTRFQTPVGPWSLTRDIALDYRNKEQKISIGPHCWLNPNAELCVPQTID AGAEGRAVVNLNRFDLAMLKPFMPETTQASGIFTGKADVAWDTTKEGLPQGSITLSGRNVQVTQTVNDAALPVAFQTLNL TAELRNNRAELGWTIRLTNNGQFDGQVQVTDPQGRRNLGGNVNIRNFNLAMINPIFTRGEKAAGMVSANLRLGGDVQSPQ LFGQLQVTGVDIDGNFMPFDMQPSQLAVNFNGMRSTLAGTVRTQQGEIYLNGDADWSQIENWRARVTAKGSKVRITVPPM VRMDVSPDVVFEATPNLFTLDGRVDVPWARIVVHDLPESAVGVSSDVVMLNDNLQPEEPKTASIPINSNLIVHVGNNVRI DAFGLKARLTGDLNVVQDKQGLGLNGQINIPEGRFHAYGQDLIVRKGELLFSGPPDQPYLNIEAIRNPDATEDDVIAGVR VTGLADEPKAEIFSDPAMSQQAALSYLLRGQGLESDQSDSAAMTSMLIGLGVAQSGQIVGKIGETFGVSNLALDTQGVGD SSQVVVSGYVLPGLQVKYGVGIFDSIATLTLRYRLMPKLYLEAVSGVDQALDLLYQFEF
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (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: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110592 / Symmetry type: POINT
RefinementHighest resolution: 3.82 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036601
ELECTRON MICROSCOPYf_angle_d0.5138981
ELECTRON MICROSCOPYf_dihedral_angle_d4.431914
ELECTRON MICROSCOPYf_chiral_restr0.044998
ELECTRON MICROSCOPYf_plane_restr0.0041179

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