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- EMDB-48837: Cryo-EM structure of F. johnsoniae BamAD -

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Basic information

Entry
Database: EMDB / ID: EMD-48837
TitleCryo-EM structure of F. johnsoniae BamAD
Map datadeepEMhancer sharpened map
Sample
  • Complex: BamAD complex
    • Protein or peptide: DNA uptake lipoprotein-like protein
  • Protein or peptide: Surface antigen (D15)
KeywordsBAM complex / BamA / BamD / outer-membrane proteins / OMP / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane assembly / cell outer membrane
Similarity search - Function
Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain ...Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DNA uptake lipoprotein-like protein / Surface antigen (D15)
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDeme JC / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: To Be Published
Title: An extended BAM complex in the Bacteroidota
Authors: Liu X / Orenday Tapia L / Deme JC / Lea SM / Berks BC
History
DepositionJan 28, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48837.png

Downloads & links

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Map

FileDownload / File: emd_48837.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0018210866 - 1.8808244
Average (Standard dev.)0.0003291367 (±0.012629725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48837_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_48837_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: global b factor sharpened map

Fileemd_48837_additional_2.map
Annotationglobal b factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer version of volume from refinement focussed on...

Fileemd_48837_additional_3.map
AnnotationDeepEMhancer version of volume from refinement focussed on second, unassigned, outer membrane barrel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_48837_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_48837_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BamAD complex

EntireName: BamAD complex
Components
  • Complex: BamAD complex
    • Protein or peptide: DNA uptake lipoprotein-like protein
  • Protein or peptide: Surface antigen (D15)

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Supramolecule #1: BamAD complex

SupramoleculeName: BamAD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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Macromolecule #1: DNA uptake lipoprotein-like protein

MacromoleculeName: DNA uptake lipoprotein-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101
Molecular weightTheoretical: 30.219377 KDa
SequenceString: MKKIVSLLIV AALFCSCSEY QKALKNEDVA AKFEVATKMY DAGKYNKAIR LFEQLAPTYR GKPQAEKLFY MFSQSYYKTK QYYLAGYQF ESFVSGYPRS EKVQEAAFLG AYSYSKLAPV YSLDQADTVK ALDKLQAFID NYPNSEYLAQ ANESVKILNG K LEKKAYEN ...String:
MKKIVSLLIV AALFCSCSEY QKALKNEDVA AKFEVATKMY DAGKYNKAIR LFEQLAPTYR GKPQAEKLFY MFSQSYYKTK QYYLAGYQF ESFVSGYPRS EKVQEAAFLG AYSYSKLAPV YSLDQADTVK ALDKLQAFID NYPNSEYLAQ ANESVKILNG K LEKKAYEN AKGYNTISDY KSALVAFDNF IADFPGTPLK EDALFYKYDS AYQLAINSVP SKMEERLHVA QTAYANLMKY KS DTKYKEK ADQMNARVET DLQKFTK

UniProtKB: DNA uptake lipoprotein-like protein

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Macromolecule #2: Surface antigen (D15)

MacromoleculeName: Surface antigen (D15) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101
Molecular weightTheoretical: 101.49032 KDa
SequenceString: MLQKRIPQII CTLLLLGSFS QIKAQDRVPF DQGKKYTLAK VSVVGKISFN EQTVVTFSGL QKGQEITVPG EEITSAIKKL GKLGLFDEI AFYINKVEND SIYLDLNIVE LPKLNEVKIT GVKKSKVEGL IKDNNLTKNK IVNENLITTT KNYIENKYKK D GFYNTKVV ...String:
MLQKRIPQII CTLLLLGSFS QIKAQDRVPF DQGKKYTLAK VSVVGKISFN EQTVVTFSGL QKGQEITVPG EEITSAIKKL GKLGLFDEI AFYINKVEND SIYLDLNIVE LPKLNEVKIT GVKKSKVEGL IKDNNLTKNK IVNENLITTT KNYIENKYKK D GFYNTKVV ITTTPDTTAG NQVNMLVRVD KGDKVKISSI DFTGNKQLSD SKLRAAMKDT KQKNVLRVFK ASKFIPEKYK TD LEKVIAS YKEKGYRDAR IIYDSVIYNK KKNMLAIKID VEEGNKYYFG NIKFLGNTVY SDQQLNRYLG IKKGETYNGV LLE KRIADN TKPDGEDITN LYQNNGYLFS KINAVEVKTV NDTIDFEIRI TEGPIAYFNK IYVTGNDKTN DHVIYRELRT KPGN KYSKE ELVRTIREIG QLGFFDPESI KPEFRNVDPA AGTVDIEYQL VEKGSSQVEL QGGYGGGGFI GTLGLSFNNF SARKL FDKD AYKPLPMGDG QKVALRLQGS TYFQTYSLSF SEPWFGGKKP VQFSSSISYS KQFNYNYSSR DVNRNQSFNI FTVQVG LAK RLTVPDDYFV LSQSVSYQHY DLNNYYTGLF TFGNGASRNL AYTIGLSRSN KGVNPIFPTY GSEFSISAKV TPPYSLF NN INYGDLQNQK EYKTQYTGTT TTTGIDGQAI NPGDYTKTET VNGQSGTVSV GSDYKSADTD VGKVDQKKYN WLEYYKVK F KADWYTKIYG KLVLRTLTEF GFLGAYDQSR GVVPFERFYL GGDGMANYSM DGRETIQLRG YPNNSLTPII EDRNSSRYG QQIGATIYNK FSMELRYPIT LKSSASIYAL TFLEAGSSYP TFKDYNPFDL NRSAGAGLRV FMPAFGLLGI DFGYGFDALP GSTTNKANG WETHFIIGQQ F

UniProtKB: Surface antigen (D15)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 534368
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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