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- EMDB-52305: OmpK35 in complex with bacteriocin KlebG -

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Basic information

Entry
Database: EMDB / ID: EMD-52305
TitleOmpK35 in complex with bacteriocin KlebG
Map dataMap used for model building from local refinement in cryosparc
Sample
  • Complex: Trimeric outer membrane protein OmpK35 in amphipol, complexed with the bacteriocin KlebG
    • Protein or peptide: OmpK35 porin
    • Protein or peptide: Klebicin G
KeywordsOuter membrane protein / bacteriocin / complex / receptor / toxin / MEMBRANE PROTEIN
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Biological speciesKlebsiella quasipneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWebby MN / Kleanthous C / Sun A / Housden NG
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: OmpK35 in complex with bacteriocin KlebG
Authors: Webby MN / Kleanthous C / Sun A / Housden NG
History
DepositionDec 10, 2024-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52305.png

Downloads & links

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Map

FileDownload / File: emd_52305.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap used for model building from local refinement in cryosparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 288 pix.
= 246.24 Å		0.86 Å/pix.
x 288 pix.
= 246.24 Å		0.86 Å/pix.
x 288 pix.
= 246.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41
Minimum - Maximum-2.4629269 - 3.4929001
Average (Standard dev.)0.00116896 (±0.08456838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 246.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_52305_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_52305_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric outer membrane protein OmpK35 in amphipol, complexed wit...

EntireName: Trimeric outer membrane protein OmpK35 in amphipol, complexed with the bacteriocin KlebG
Components
  • Complex: Trimeric outer membrane protein OmpK35 in amphipol, complexed with the bacteriocin KlebG
    • Protein or peptide: OmpK35 porin
    • Protein or peptide: Klebicin G

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Supramolecule #1: Trimeric outer membrane protein OmpK35 in amphipol, complexed wit...

SupramoleculeName: Trimeric outer membrane protein OmpK35 in amphipol, complexed with the bacteriocin KlebG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella quasipneumoniae (bacteria) / Strain: QMP M1-977

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Macromolecule #1: OmpK35 porin

MacromoleculeName: OmpK35 porin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella quasipneumoniae (bacteria)
Molecular weightTheoretical: 39.572059 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMKRNILAVV IPALLVAGAA NAAEIYNKNG NKLDFYGKMV GEHVWTTNGK TSSDDTTYAR IGLKGETQIN DQLTGYGQWE YNMDASNVE GSQPTKTRLA FAGLKAGEYG SFDYGRNYGA IYDVEAATDM LVEWGGDGWN YTDNYMTGRT NGVATYRNSD F FGLVDGLS ...String:
MMKRNILAVV IPALLVAGAA NAAEIYNKNG NKLDFYGKMV GEHVWTTNGK TSSDDTTYAR IGLKGETQIN DQLTGYGQWE YNMDASNVE GSQPTKTRLA FAGLKAGEYG SFDYGRNYGA IYDVEAATDM LVEWGGDGWN YTDNYMTGRT NGVATYRNSD F FGLVDGLS FALQYQGKND HDRSIHKQNG DGFSTAATYA FDNGIALSAG YSGSNRSVDQ KADGNGDKAE AWATSAKYDA NN VYAAVMY SQTYNMTPEN QGNYFAGKTQ NFEAVVQYQF DFGLRPSIGY VQTKGKDLQA RGGFSGGDAD LVKYVEVGTW YYF NKNMNV YAAYKFNQLD DNAYTREAGV ATDDQAAVGI VYQF

UniProtKB: OmpK35 porin

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Macromolecule #2: Klebicin G

MacromoleculeName: Klebicin G / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella quasipneumoniae (bacteria)
Molecular weightTheoretical: 80.204719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGGGFNYNGE GATGTGLDRD PYVRDSNGNA IGVKSGYHAE SYGTSSPALG PNGAIQITAG VIAVPGDKPR PDGGSGGGNT VNTGPAGQL LVMNKGQLGY WETRSTGAGN NEHNTSVFVA VGPSEAEKTA SAEKALKEKQ QAEAAAKDFA AKTAAASATA E KERQQAIA ...String:
MGGGFNYNGE GATGTGLDRD PYVRDSNGNA IGVKSGYHAE SYGTSSPALG PNGAIQITAG VIAVPGDKPR PDGGSGGGNT VNTGPAGQL LVMNKGQLGY WETRSTGAGN NEHNTSVFVA VGPSEAEKTA SAEKALKEKQ QAEAAAKDFA AKTAAASATA E KERQQAIA AATAAGQHQS VSDARNSLNN ATSDVSRLKS AADSALQEAK AKRKAAIDAV PVATQAENKY QELQQKIKGL KL KNGEYGT EKWEIIGSNK EHDHWGYRFY PSGITKAQVD VAQSDAVNKR NQATSLASQA TAAEQDSLKA TAAYNAAETR RQA AQAALN SAEQAAAAER KRQEAEAAAA AAAEKKRQAD AVAKAAEEAR AAAEKARLMQ ERQAAADKLK STDIQSVRGI PSTA SPAAS PISWAVASLG GISLDSVTAG KAWTQIAEVM AKLRGIAGAS LVGPVVATAV GLFWSRDVGI GSDVVPGRDI SGLMP GDAL SLPDLATLIK AADSKTGVSM PVRGRIIVRE GDYLESQFVR TPVAGSVPVV RATLDKATGY WGYTLPAIQG VPGQTI LVS PSDAPGVNAP LGLAGPVPLP ETIIHTGGQT TVPQGGTVTV SPVIGEVDFR DLILVFPPES GLKPLYVMAM ESKRNKP GK ATGKGKPVGD KWLDDAGKDS GAPIPDRIAD KLRDKEFKSF DDFRKAVWEE VSKDPELSKN LNPSNKSSVS KGYSPFTP K NQQVGGRKVY ELHHDKPISQ GGEVYDMDNI RVTTPKRHID IHRGK

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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

Concentration0.4 mg/mL
BufferpH: 7.9 / Details: 50 mM sodium phosphate, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Detailsouter membrane protein transferred into amphipol for cryo-EM

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11510 / Average exposure time: 8.0 sec. / Average electron dose: 57.46 e/Å2
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: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 190000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 624472
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial docking was done in chimera and refined in phenix, inspecting in coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9hn2:
OmpK35 in complex with bacteriocin KlebG

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