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- EMDB-21900: Cryo-EM structure of E. Coli OmpF -

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Basic information

Entry
Database: EMDB / ID: EMD-21900
TitleCryo-EM structure of E. Coli OmpF
Map data
SampleOmpF:
Outer membrane porin F / ligand
Function / homology
Function and homology information


colicin transmembrane transporter activity / ion transmembrane transporter activity / ion channel complex / porin activity / pore complex / protein homotrimerization / ion transmembrane transport / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding ...colicin transmembrane transporter activity / ion transmembrane transporter activity / ion channel complex / porin activity / pore complex / protein homotrimerization / ion transmembrane transport / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / ion channel activity / protein N-terminus binding / lipid binding / integral component of membrane / identical protein binding
Porin domain superfamily / Porin domain, Gram-negative type / Porin, Gram-negative type, conserved site / Porin, gammaproteobacterial / Porin, Gram-negative type
Outer membrane porin F
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMorgan CE / Su C-C / Lyu M / Yu EW
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
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
History
DepositionMay 4, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wtz
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21900.map.gz / Format: CCP4 / Size: 163.6 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 350 pix.
= 378. Å
1.08 Å/pix.
x 350 pix.
= 378. Å
1.08 Å/pix.
x 350 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 1
Minimum - Maximum-5.091714 - 7.68671
Average (Standard dev.)1.1505658e-13 (±0.085303746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-5.0927.6870.000

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Supplemental data

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Sample components

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Entire OmpF

EntireName: OmpF / Number of components: 3

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Component #1: protein, OmpF

ProteinName: OmpF / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #2: protein, Outer membrane porin F

ProteinName: Outer membrane porin F / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 39.365043 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #3: ligand, water

LigandName: water / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 43793
3D reconstructionSoftware: cryoSPARC / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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