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- EMDB-79024: Cryo-EM map of crosslinked E. coli TAM Complex in DDM detergent, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-79024
TitleCryo-EM map of crosslinked E. coli TAM Complex in DDM detergent, interruption of density visible near TamA lateral gate
Map data
Sample
  • Complex: E. coli TAM Complex (TamA-TamB)
    • Protein or peptide: TamA
    • Protein or peptide: TamB
KeywordsPeriplasm / outer membrane / AsmA / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.19 Å
AuthorsSchilling MA / Reinisch KM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)MIRA-R35GM131715 United States
CitationJournal: To Be Published
Title: Cryo-EM map of crosslinked E. coli TAM Complex in DDM detergent, interruption of density visible near TamA lateral gate
Authors: Schilling MA / Reinisch KM
History
DepositionSep 10, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79024.png

Downloads & links

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Map

FileDownload / File: emd_79024.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 320.4 Å		1.07 Å/pix.
x 300 pix.
= 320.4 Å		1.07 Å/pix.
x 300 pix.
= 320.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0675
Minimum - Maximum-0.1167248 - 0.28333429
Average (Standard dev.)0.00077953655 (±0.012514335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_79024_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_79024_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli TAM Complex (TamA-TamB)

EntireName: E. coli TAM Complex (TamA-TamB)
Components
  • Complex: E. coli TAM Complex (TamA-TamB)
    • Protein or peptide: TamA
    • Protein or peptide: TamB

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Supramolecule #1: E. coli TAM Complex (TamA-TamB)

SupramoleculeName: E. coli TAM Complex (TamA-TamB) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Crosslinked with glutaraldehyde, in DDM detergent. For details regarding Cloning and Construct Design; Protein Purification; Cryo-EM Sample Preparation; and Cryo-EM Data Processing, please ...Details: Crosslinked with glutaraldehyde, in DDM detergent. For details regarding Cloning and Construct Design; Protein Purification; Cryo-EM Sample Preparation; and Cryo-EM Data Processing, please visit: dx.doi.org/10.17504/protocols.io.14egnp4q6v5d/v1 dx.doi.org/10.17504/protocols.io.bp2l6o86dlqe/v1 dx.doi.org/10.17504/protocols.io.261geqebjg47/v1 dx.doi.org/10.17504/protocols.io.q26g7q5k9lwz/v1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: DH5-alpha
Molecular weightTheoretical: 202.8 KDa

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Macromolecule #1: TamA

MacromoleculeName: TamA / type: protein_or_peptide / ID: 1 / Details: malE-6xHis-TEV-TamA(22-577) / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: DH5-alpha
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIKTGARIL ALSALTTMMF SASALAMAHH HHHHENLYFQ GIQANVRLQV EGLSGQLEKN VRAQLSTIES DEVTPDRRFR ARVDDAIREG LKALGYYQPT IEFDLRPPPK KGRQVLIAKV TPGVPVLIGG TDVVLRGGAR TDKDYLKLLD TRPAIGTVLN QGDYENFKKS ...String:
MKIKTGARIL ALSALTTMMF SASALAMAHH HHHHENLYFQ GIQANVRLQV EGLSGQLEKN VRAQLSTIES DEVTPDRRFR ARVDDAIREG LKALGYYQPT IEFDLRPPPK KGRQVLIAKV TPGVPVLIGG TDVVLRGGAR TDKDYLKLLD TRPAIGTVLN QGDYENFKKS LTSIALRKGY FDSEFTKAQL GIALGLHKAF WDIDYNSGER YRFGHVTFEG SQIRDEYLQN LVPFKEGDEY ESKDLAELNR RLSATGWFNS VVVAPQFDKA RETKVLPLTG VVSPRTENTI ETGVGYSTDV GPRVKATWKK PWMNSYGHSL TTSTSISAPE QTLDFSYKMP LLKNPLEQYY LVQGGFKRTD LNDTESDSTT LVASRYWDLS SGWQRAINLR WSLDHFTQGE ITNTTMLFYP GVMISRTRSR GGLMPTWGDS QRYSIDYSNT AWGSDVDFSV FQAQNVWIRT LYDRHRFVTR GTLGWIETGD FDKVPPDLRF FAGGDRSIRG YKYKSIAPKY ANGDLKGASK LITGSLEYQY NVTGKWWGAV FVDSGEAVSD IRRSDFKTGT GVGVRWESPV GPIKLDFAVP VADKDEHGLQ FYIGLGPEL

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Macromolecule #2: TamB

MacromoleculeName: TamB / type: protein_or_peptide / ID: 2 / Details: MGSS-6xHis-SQ-TamB(1-1259) / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: DH5-alpha
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQMSLWKKIS LGVVIVILLL LGSVAFLVGT TSGLHLVFKA ADRWVPGLDI GKVTGGWRDL TLSDVRYEQP GVAVKAGNLH LAVGLECLWN SSVCINDLAL KDIQVNIDSK KMPPSEQVEE EEDSGPLDLS TPYPITLTRV ALDNVNIKID DTTVSVMDFT ...String:
MGSSHHHHHH SQMSLWKKIS LGVVIVILLL LGSVAFLVGT TSGLHLVFKA ADRWVPGLDI GKVTGGWRDL TLSDVRYEQP GVAVKAGNLH LAVGLECLWN SSVCINDLAL KDIQVNIDSK KMPPSEQVEE EEDSGPLDLS TPYPITLTRV ALDNVNIKID DTTVSVMDFT SGLNWQEKTL TLKPTSLKGL LIALPKVAEV AQEEVVEPKI ENPQPDEKPL GETLKDLFSR PVLPEMTDVH LPLNLNIEEF KGEQLRVTGD TDITVSTMLL KVSSIDGNTK LDALDIDSSQ GIVNASGTAQ LSDNWPVDIT LNSTLNVEPL KGEKVKLKMG GALREQLEIG VNLSGPVDMD LRAQTRLAEA GLPLNVEVNS KQLYWPFTGE KQYQADDLKL KLTGKMTDYT LSMRTAVKGQ EIPPATITLD AKGNEQQVNL DKLTVAALEG KTELKALLDW QQAISWRGEL TLNGINTAKE FPDWPSKLNG LIKTRGSLYG GTWQMDVPEL KLTGNVKQNK VNVDGTLKGN SYMQWMIPGL HLELGPNSAE VKGELGVKDL NLDATINAPG LDNALPGLGG TAKGLVKVRG TVEAPQLLAD ITARGLRWQE LSVAQVRVEG DIKSTDQIAG KLDVRVEQIS QPDVNINLVT LNAKGSEKQH ELQLRIQGEP VSGQLNLAGS FDRKEERWKG TLSNTRFQTP VGPWSLTRDI ALDYRNKEQK ISIGPHCWLN PNAELCVPQT IDAGAEGRAV VNLNRFDLAM LKPFMPETTQ ASGIFTGKAD VAWDTTKEGL PQGSITLSGR NVQVTQTVND AALPVAFQTL NLTAELRNNR AELGWTIRLT NNGQFDGQVQ VTDPQGRRNL GGNVNIRNFN LAMINPIFTR GEKAAGMVSA NLRLGGDVQS PQLFGQLQVT GVDIDGNFMP FDMQPSQLAV NFNGMRSTLA GTVRTQQGEI YLNGDADWSQ IENWRARVTA KGSKVRITVP PMVRMDVSPD VVFEATPNLF TLDGRVDVPW ARIVVHDLPE SAVGVSSDVV MLNDNLQPEE PKTASIPINS NLIVHVGNNV RIDAFGLKAR LTGDLNVVQD KQGLGLNGQI NIPEGRFHAY GQDLIVRKGE LLFSGPPDQP YLNIEAIRNP DATEDDVIAG VRVTGLADEP KAEIFSDPAM SQQAALSYLL RGQGLESDQS DSAAMTSMLI GLGVAQSGQI VGKIGETFGV SNLALDTQGV GDSSQVVVSG YVLPGLQVKY GVGIFDSIAT LTLRYRLMPK LYLEAVSGVD QALDLLYQFE F

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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

Concentration14 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 10.0 kPa / Details: 25 mA, Sputter Coater, (SCD005, Bal-Tec)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV
DetailsTamA and TamB purified from 12 L and 28 L cells, respectively. Both proteins were incubated overnight at 10 degrees at a TamA:TamB molar ratio of approximately 1.7-2.5:1. 6-22 mg/mL final.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Details2,167 images collected with 30 degree stage tilt.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 27073 / Average exposure time: 2.696 sec. / Average electron dose: 51.29 e/Å2
Details: 2,167 images collected with 30 degree stage tilt. Dose-fractionated into 50 frames of 0.054 seconds each. Super-resolution mode (0.534 Angstroms/pixel)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-Uniform Refinement
Details: 745,024 particles underwent Ab Initio Reconstruction (above), followed by Heterogenous Refinement (300 voxel refinement box, 12 Angstrom initial resolution). Best volume then underwent Non- ...Details: 745,024 particles underwent Ab Initio Reconstruction (above), followed by Heterogenous Refinement (300 voxel refinement box, 12 Angstrom initial resolution). Best volume then underwent Non-Uniform Refinement (above).
Number images used: 623763
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Ab Initio Reconstruction
Details: Ab Initio Reconstruction 2 Classes Maximum/Initial Resolution: 5/12 Angstroms Initial/Final Minibatch Size: 300/1000
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-Uniform Refinement
Details: Non-Uniform Refinement Non-Uniform AWF: 1.5 Minimize over per-particle scale specified
FSC plot (resolution estimation)

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