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

Open data

ID or keywords:


Basic information

Database: EMDB / ID: EMD-22529
TitleOsmoporin OmpC from E.coli K12
Map data
SampleOsmoporin OmpC:
Outer membrane protein C
Function / homologyPorin, Gram-negative type / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / Porin domain superfamily / porin activity / pore complex / ion transmembrane transport / cell outer membrane / Outer membrane protein C
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsLyu M / Su C / Morgan CE / Bolla JR / Robinson CV / Yu EW
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.
Validation ReportSummary, Full report, XML, About validation report
DepositionSep 1, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • 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:
Supplemental images

Downloads & links


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

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



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
Contour LevelBy AUTHOR: 0.378 / Movie #1: 0.4
Minimum - Maximum-2.7008746 - 3.235201
Average (Standard dev.)-2.6177576e-13 (±0.2120853)
SymmetrySpace group: 1


Map geometry
Axis orderZYX
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
start NX/NY/NZ107101134
MAP C/R/S321
start NC/NR/NS134101107
D min/max/mean-2.7013.235-0.000

Supplemental data

Additional map: #1

Projections & Slices


Slices (1/2)
Density Histograms

Sample components

Entire Osmoporin OmpC

EntireName: Osmoporin OmpC / Number of components: 2

Component #1: protein, Osmoporin OmpC

ProteinName: Osmoporin OmpC / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli) / Strain: K-12

Component #2: protein, Outer membrane protein C

ProteinName: Outer membrane protein C / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 38.336242 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: K-12

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.7 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 68628
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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