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- EMDB-22529: Osmoporin OmpC from E.coli K12 -

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Basic information

Entry
Database: EMDB / ID: EMD-22529
TitleOsmoporin OmpC from E.coli K12
Map data
Sample
  • Complex: Osmoporin OmpC
    • Protein or peptide: Outer membrane protein C
KeywordsOsmoporin OmpC / TRANSPORT PROTEIN
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Outer membrane protein C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsLyu M / Su C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Methods / Year: 2021
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
History
DepositionSep 1, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jz3
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22529.png

Downloads & links

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Map

FileDownload / File: emd_22529.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 141 pix.
= 152.28 Å		1.08 Å/pix.
x 139 pix.
= 150.12 Å		1.08 Å/pix.
x 86 pix.
= 92.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.378 / Movie #1: 0.4
Minimum - Maximum-2.7008746 - 3.235201
Average (Standard dev.)-0.000000000000262 (±0.2120853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin101134107
Dimensions13986141
Spacing14113986
CellA: 152.28 Å / B: 150.12001 Å / C: 92.880005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z14113986
origin x/y/z0.0000.0000.000
length x/y/z152.280150.12092.880
α/β/γ90.00090.00090.000
start NX/NY/NZ107101134
NX/NY/NZ14113986
MAP C/R/S321
start NC/NR/NS134101107
NC/NR/NS86139141
D min/max/mean-2.7013.235-0.000

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Supplemental data

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Additional map: #1

Fileemd_22529_additional_1.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 : Osmoporin OmpC

EntireName: Osmoporin OmpC
Components
  • Complex: Osmoporin OmpC
    • Protein or peptide: Outer membrane protein C

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Supramolecule #1: Osmoporin OmpC

SupramoleculeName: Osmoporin OmpC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12

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Macromolecule #1: Outer membrane protein C

MacromoleculeName: Outer membrane protein C / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 38.336242 KDa
SequenceString: AEVYNKDGNK LDLYGKVDGL HYFSDNKDVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGNPSGE G FTSGVTNN ...String:
AEVYNKDGNK LDLYGKVDGL HYFSDNKDVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGNPSGE G FTSGVTNN GRDALRQNGD GVGGSITYDY EGFGIGGAIS SSKRTDAQNT AAYIGNGDRA ETYTGGLKYD ANNIYLAAQY TQ TYNATRV GSLGWANKAQ NFEAVAQYQF DFGLRPSLAY LQSKGKNLGR GYDDEDILKY VDVGATYYFN KNMSTYVDYK INL LDDNQF TRDAGINTDN IVALGLVYQF

UniProtKB: Outer membrane protein C

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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

Concentration0.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68628
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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