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- EMDB-69220: TamA complex with TamB DUF490 in detergent micelles. -

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Basic information

Entry
Database: EMDB / ID: EMD-69220
TitleTamA complex with TamB DUF490 in detergent micelles.
Map dataMap of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job and sharpened with EMReady2.
Sample
  • Complex: Complex of translocation and assembly module subunit A (TamA) with translocation and assembly module subunit B DUF490 (TamB DUF490).
    • Protein or peptide: Translocation and assembly module subunit TamB
    • Protein or peptide: Translocation and assembly module subunit TamA
Keywordsbeta barrel / TAM / complex / OMP / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsAdamson LSR / Doyle MT / Grosas AB
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP260100880 Australia
CitationJournal: 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, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69220.png

Downloads & links

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Map

FileDownload / File: emd_69220.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job and sharpened with EMReady2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-0.10850844 - 16.497564000000001
Average (Standard dev.)-0.023261746 (±0.2726025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of TamABDUF490 in lmng micelles directly output...

Fileemd_69220_additional_1.map
AnnotationMap of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job sharpened by cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of TamABDUF490 in lmng micelles directly...

Fileemd_69220_additional_2.map
AnnotationUnsharpened map of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map of TamABDUF490 in lmng micelles directly output...

Fileemd_69220_additional_3.map
AnnotationMap of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job and sharpened by locscale2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of TamABDUF490 in lmng micelles...

Fileemd_69220_half_map_1.map
AnnotationHalf map A of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of TamABDUF490 in lmng micelles...

Fileemd_69220_half_map_2.map
AnnotationHalf map B of TamABDUF490 in lmng micelles directly output from final cryoSPARC local refine job.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of translocation and assembly module subunit A (TamA) wit...

EntireName: Complex of translocation and assembly module subunit A (TamA) with translocation and assembly module subunit B DUF490 (TamB DUF490).
Components
  • Complex: Complex of translocation and assembly module subunit A (TamA) with translocation and assembly module subunit B DUF490 (TamB DUF490).
    • Protein or peptide: Translocation and assembly module subunit TamB
    • Protein or peptide: Translocation and assembly module subunit TamA

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Supramolecule #1: Complex of translocation and assembly module subunit A (TamA) wit...

SupramoleculeName: Complex of translocation and assembly module subunit A (TamA) with translocation and assembly module subunit B DUF490 (TamB DUF490).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 112.8 KDa

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Macromolecule #1: Translocation and assembly module subunit TamB

MacromoleculeName: Translocation and assembly module subunit TamB / type: protein_or_peptide / ID: 1
Details: Residues 837-1259 of E. coli Translocation and Assembly Module subunit B.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.738664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GSNLGGNVNI RNFNLAMINP IFTRGEKAAG MVSANLRLGG DVQSPQLFGQ LQVTGVDID GNFMPFDMQP SQLAVNFNGM RSTLAGTVRT QQGEIYLNGD ADWSQIENWR ARVTAKGSKV RITVPPMVRM D VSPDVVFE ...String:
AWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GSNLGGNVNI RNFNLAMINP IFTRGEKAAG MVSANLRLGG DVQSPQLFGQ LQVTGVDID GNFMPFDMQP SQLAVNFNGM RSTLAGTVRT QQGEIYLNGD ADWSQIENWR ARVTAKGSKV RITVPPMVRM D VSPDVVFE ATPNLFTLDG RVDVPWARIV VHDLPESAVG VSSDVVMLND NLQPEEPKTA SIPINSNLIV HVGNNVRIDA FG LKARLTG DLNVVQDKQG LGLNGQINIP EGRFHAYGQD LIVRKGELLF SGPPDQPYLN IEAIRNPDAT EDDVIAGVRV TGL ADEPKA EIFSDPAMSQ QAALSYLLRG QGLESDQSDS AAMTSMLIGL GVAQSGQIVG KIGETFGVSN LALDTQGVGD SSQV VVSGY VLPGLQVKYG VGIFDSIATL TLRYRLMPKL YLEAVSGVDQ ALDLLYQFEF

UniProtKB: Translocation and assembly module subunit TamB

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Macromolecule #2: Translocation and assembly module subunit TamA

MacromoleculeName: Translocation and assembly module subunit TamA / type: protein_or_peptide / ID: 2
Details: E. coli Translocation and Assembly Module subunit A.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64.225852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AHHHHHHHHG GSGGSGGNVR LQVEGLSGQL EKNVRAQLST IESDEVTPDR RFRARVDDAI REGLKALGYY QPTIEFDLRP PPKKGRQVL IAKVTPGVPV LIGGTDVVLR GGARTDKDYL KLLDTRPAIG TVLNQGDYEN FKKSLTSIAL RKGYFDSEFT K AQLGIALG ...String:
AHHHHHHHHG GSGGSGGNVR LQVEGLSGQL EKNVRAQLST IESDEVTPDR RFRARVDDAI REGLKALGYY QPTIEFDLRP PPKKGRQVL IAKVTPGVPV LIGGTDVVLR GGARTDKDYL KLLDTRPAIG TVLNQGDYEN FKKSLTSIAL RKGYFDSEFT K AQLGIALG LHKAFWDIDY NSGERYRFGH VTFEGSQIRD EYLQNLVPFK EGDEYESKDL AELNRRLSAT GWFNSVVVAP QF DKARETK VLPLTGVVSP RTENTIETGV GYSTDVGPRV KATWKKPWMN SYGHSLTTST SISAPEQTLD FSYKMPLLKN PLE QYYLVQ GGFKRTDLND TESDSTTLVA SRYWDLSSGW QRAINLRWSL DHFTQGEITN TTMLFYPGVM ISRTRSRGGL MPTW GDSQR YSIDYSNTAW GSDVDFSVFQ AQNVWIRTLY DRHRFVTRGT LGWIETGDFD KVPPDLRFFA GGDRSIRGYK YKSIA PKYA NGDLKGASKL ITGSLEYQYN VTGKWWGAVF VDSGEAVSDI RRSDFKTGTG VGVRWESPVG PIKLDFAVPV ADKDEH GLQ FYIGLGPEL

UniProtKB: Translocation and assembly module subunit TamA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.46 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMC4H11NO3Tris
0.003 %C47H88O22LMNG

Details: 50 mM Tris pH 8 150 mM NaCl 0.003% LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 uL sample applied for blotting. Wait time of 60s, blot time of 3s with a blot force of 9..
DetailsSample was prepared in LMNG micelles.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 80583
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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