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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 dataE. coli OmpF in nanodisc
Sample
  • Complex: OmpF
    • Protein or peptide: Outer membrane porin F
  • Ligand: water
Keywordsouter membrane porin / omp / ompf / MEMBRANE PROTEIN
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
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
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.
History
DepositionMay 4, 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: 1
  • Imaged by UCSF Chimera
  • Download
  • 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

emd_21900.png

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)
AnnotationE. coli OmpF in nanodisc
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 1
Minimum - Maximum-5.091714 - 7.68671
Average (Standard dev.)0.000000000000115 (±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
Components
  • Complex: OmpF
    • Protein or peptide: Outer membrane porin F
  • Ligand: water

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Supramolecule #1: OmpF

SupramoleculeName: OmpF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Outer membrane porin F

MacromoleculeName: Outer membrane porin F / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 39.365043 KDa
SequenceString: MMKRNILAVI VPALLVAGTA NAAEIYNKDG NKVDLYGKAV GLHYFSKGNG ENSYGGNGDM TYARLGFKGE TQINSDLTGY GQWEYNFQG NNSEGADAQT GNKTRLAFAG LKYADVGSFD YGRNYGVVYD ALGYTDMLPE FGGDTAYSDD FFVGRVGGVA T YRNSNFFG ...String:
MMKRNILAVI VPALLVAGTA NAAEIYNKDG NKVDLYGKAV GLHYFSKGNG ENSYGGNGDM TYARLGFKGE TQINSDLTGY GQWEYNFQG NNSEGADAQT GNKTRLAFAG LKYADVGSFD YGRNYGVVYD ALGYTDMLPE FGGDTAYSDD FFVGRVGGVA T YRNSNFFG LVDGLNFAVQ YLGKNERDTA RRSNGDGVGG SISYEYEGFG IVGAYGAADR TNLQEAQPLG NGKKAEQWAT GL KYDANNI YLAANYGETR NATPITNKFT NTSGFANKTQ DVLLVAQYQF DFGLRPSIAY TKSKAKDVEG IGDVDLVNYF EVG ATYYFN KNMSTYVDYI INQIDSDNKL GVGSDDTVAV GIVYQF

UniProtKB: Outer membrane porin F

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 36 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43793
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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