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- EMDB-48836: Cryo-EM structure of F. johnsoniae BamAP -

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Basic information

Entry
Database: EMDB / ID: EMD-48836
TitleCryo-EM structure of F. johnsoniae BamAP
Map datadeepEMhancer sharpened map
Sample
  • Complex: BamAP complex
    • Protein or peptide: Surface antigen (D15)
    • Protein or peptide: CarboxypepD_reg-like domain-containing protein
KeywordsBamAP complex / BamA / BamP / 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 BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
CarboxypepD_reg-like domain-containing protein / Surface antigen (D15)
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48836.png

Downloads & links

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Map

FileDownload / File: emd_48836.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: 0.2
Minimum - Maximum-0.0017948509 - 2.080528
Average (Standard dev.)0.0003497251 (±0.013360993)
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_48836_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_48836_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_48836_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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Half map: half map 1

Fileemd_48836_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_48836_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 : BamAP complex

EntireName: BamAP complex
Components
  • Complex: BamAP complex
    • Protein or peptide: Surface antigen (D15)
    • Protein or peptide: CarboxypepD_reg-like domain-containing protein

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Supramolecule #1: BamAP complex

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

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Macromolecule #1: Surface antigen (D15)

MacromoleculeName: Surface antigen (D15) / 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: 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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Macromolecule #2: CarboxypepD_reg-like domain-containing protein

MacromoleculeName: CarboxypepD_reg-like domain-containing protein / 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: 28.413742 KDa
SequenceString: MKNKLGVFVV CLFCQIMLGQ NGTRKSLHGQ VTNKSLAIES GYVMNINAKS RTFIGPGGLF DILAQPKDTL LFTGIAFQSK KIVLTEKDC SQILFSVSLD LVSNELKEVL VRKDLKVKSL DSNTQKYVDM QFEDDRQSTA KNTVMYSDQT IKYGTDFVRI F KDVKKLLS ...String:
MKNKLGVFVV CLFCQIMLGQ NGTRKSLHGQ VTNKSLAIES GYVMNINAKS RTFIGPGGLF DILAQPKDTL LFTGIAFQSK KIVLTEKDC SQILFSVSLD LVSNELKEVL VRKDLKVKSL DSNTQKYVDM QFEDDRQSTA KNTVMYSDQT IKYGTDFVRI F KDVKKLLS KNNEKEEVIS DIAFVEYSKA NFKPDFYTKT LGLKPDEVDL FLMFCSNDPE SKRHLNEDQK FELIDFLINK NA EFKKVNA AQ

UniProtKB: CarboxypepD_reg-like domain-containing protein

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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: 55.7 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96076
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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