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- EMDB-9357: Outer Membrane Cytochrome S Filament from Geobacter Sulfurreducens -

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Basic information

Entry
Database: EMDB / ID: EMD-9357
TitleOuter Membrane Cytochrome S Filament from Geobacter Sulfurreducens
Map data
Sample
  • Organelle or cellular component: Outer Membrane Cytochrome S filament as a bacterial nanowire
    • Protein or peptide: C-type cytochrome OmcS
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION
Function / homologyMultiheme cytochrome superfamily / cell outer membrane / oxidoreductase activity / cell surface / metal ion binding / C-type cytochrome OmcS
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria) / Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFilman DJ / Marino SF / Ward JE / Yang L / Mester Z / Bullitt E / Lovley DR / Strauss M
Funding support United States, 1 items
OrganizationGrant numberCountry
Other governmentN00014-16-1-2526 United States
CitationJournal: Commun Biol / Year: 2019
Title: Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire.
Authors: David J Filman / Stephen F Marino / Joy E Ward / Lu Yang / Zoltán Mester / Esther Bullitt / Derek R Lovley / Mike Strauss /
Abstract: Electrically conductive pili from species, termed bacterial nanowires, are intensely studied for their biological significance and potential in the development of new materials. Using cryo-electron ...Electrically conductive pili from species, termed bacterial nanowires, are intensely studied for their biological significance and potential in the development of new materials. Using cryo-electron microscopy, we have characterized nanowires from conductive pili preparations that are composed solely of head-to-tail stacked monomers of the six-heme C-type cytochrome OmcS. The unique fold of OmcS - closely wrapped around a continuous stack of hemes that can serve as an uninterrupted path for electron transport - generates a scaffold that supports the unbranched chain of hemes along the central axis of the filament. We present here, at 3.4 Å resolution, the structure of this cytochrome-based filament and discuss its possible role in long-range biological electron transport.
History
DepositionDec 17, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJul 3, 2019-
UpdateSep 11, 2019-
Current statusSep 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nef
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nef
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9357.png

Downloads & links

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Map

FileDownload / File: emd_9357.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.13718002 - 0.2536325
Average (Standard dev.)0.0005612817 (±0.0071339365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-100-99-100
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S312
start NC/NR/NS-99-100-100
NC/NR/NS200200200
D min/max/mean-0.1370.2540.001

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Supplemental data

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Sample components

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Entire : Outer Membrane Cytochrome S filament as a bacterial nanowire

EntireName: Outer Membrane Cytochrome S filament as a bacterial nanowire
Components
  • Organelle or cellular component: Outer Membrane Cytochrome S filament as a bacterial nanowire
    • Protein or peptide: C-type cytochrome OmcS
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Outer Membrane Cytochrome S filament as a bacterial nanowire

SupramoleculeName: Outer Membrane Cytochrome S filament as a bacterial nanowire
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacter sulfurreducens (bacteria)

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Macromolecule #1: C-type cytochrome OmcS

MacromoleculeName: C-type cytochrome OmcS / type: protein_or_peptide / ID: 1
Details: SIX-HEME MULTIHEME C-TYPE CYTOCHROME, PROTEIN FIBRIL
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 42.986008 KDa
SequenceString: FHSGGVAECE GCHTMHNSLG GAVMNSATAQ FTTGPMLLQG ATQSSSCLNC HQHAGDTGPS SYHISTAEAD MPAGTAPLQM TPGGDFGWV KKTYTWNVRG LNTSEGERKG HNIVAGDYNY VADTTLTTAP GGTYPANQLH CSSCHDPHGK YRRFVDGSIA T TGLPIKNS ...String:
FHSGGVAECE GCHTMHNSLG GAVMNSATAQ FTTGPMLLQG ATQSSSCLNC HQHAGDTGPS SYHISTAEAD MPAGTAPLQM TPGGDFGWV KKTYTWNVRG LNTSEGERKG HNIVAGDYNY VADTTLTTAP GGTYPANQLH CSSCHDPHGK YRRFVDGSIA T TGLPIKNS GSYQNSNDPT AWGAVGAYRI LGGTGYQPKS LSGSYAFANQ VPAAVAPSTY NRTEATTQTR VAYGQGMSEW CA NCHTDIH NSAYPTNLRH PAGNGAKFGA TIAGLYNSYK KSGDLTGTQA SAYLSLAPFE EGTADYTVLK GHAKIDDTAL TGA DATSNV NCLSCHRAHA SGFDSMTRFN LAYEFTTIAD ASGNSIYGTD PNTSSLQGRS VNEMTAAYYG RTADKFAPYQ RALC NKCHA KD

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 6 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample contained thick (4nm) and thin (3nm) filaments. This reconstruction is of the thick filaments.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 47.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.01 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 462964

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Atomic model buiding 1

DetailsAtomic model was built de novo visually and repeatedly rebuilt visually using Coot and SPDBV. After each round of manual rebuilding, the parameters of the atomic model underwent stereochemically restrained reciprocal space refinement, using either Refmac5 or Phenix.autobuild or both, using as a reference the amplitudes and phases of the Fourier transform of a portion of the cryoEM reconstruction. For convenience, a single-subunit model was initially built to fit an approximation of the reference map in space group P4(3), which was subsequently replaced by a three-subunit model, using the authentic helical parameters of the map. one of the two axial ligands for HEM 505 is ne2 of his 41 from a neighboring helical-symmetry-related protein chain.
RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: maximum likelihood with phases
Output model

PDB-6nef:
Outer Membrane Cytochrome S Filament from Geobacter Sulfurreducens

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