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

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Entry
Database: PDB / ID: 6nef
TitleOuter Membrane Cytochrome S Filament from Geobacter Sulfurreducens
ComponentsC-type cytochrome OmcS
KeywordsPROTEIN FIBRIL / Conductive / filament / nanowire / SIX-HEME MULTIHEME C-TYPE CYTOCHROME
Function / homologyMultiheme cytochrome superfamily / cell outer membrane / oxidoreductase activity / cell surface / metal ion binding / HEME C / C-type cytochrome OmcS
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFilman, D.J. / Marino, S.F. / Ward, J.E. / Yang, L. / Mester, Z. / Bullitt, E. / Lovley, D.R. / Strauss, M.
Funding support United States, 1items
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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Sep 11, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

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  • Biological unit as representative helical assembly
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Assembly

Deposited unit
A: C-type cytochrome OmcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7218
Polymers42,9861
Non-polymers3,7357
Water00
1
A: C-type cytochrome OmcS
hetero molecules
x 9


Theoretical massNumber of molelcules
Total (without water)420,49272
Polymers386,8749
Non-polymers33,61863
Water0
TypeNameSymmetry operationNumber
helical symmetry operation9
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 9 / Rise per n subunits: 47.5 Å / Rotation per n subunits: 83.01 °)
DetailsSOME OBSERVED FILAMENTS ARE HUNDREDS OF SUBUNITS LONG

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Components

#1: Protein C-type cytochrome OmcS / Outer membrane cytochrome S


Mass: 42986.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: SIX-HEME MULTIHEME C-TYPE CYTOCHROME, PROTEIN FIBRIL
Source: (natural) Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA / References: UniProt: Q74A86
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Outer Membrane Cytochrome S filament as a bacterial nanowire
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Geobacter sulfurreducens (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample contained thick (4nm) and thin (3nm) filaments. This reconstruction is of the thick filaments.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0238 / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.7 betaimage acquisition
4RELION3CTF correction
7Cootmodel fitting
14REFMAC5.8.0238model refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 83.01 ° / Axial rise/subunit: 47.5 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462964 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: maximum likelihood with phases
Details: Atomic 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 ...Details: Atomic 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.
RefinementHighest resolution: 3.42 Å
Details: ONE OF THE TWO AXIAL LIGANDS FOR HEM 505 IS NE2 OF HIS 41 FROM A NEIGHBORING HELICAL-SYMMETRY-RELATED PROTEIN CHAIN
Refinement stepCycle: 1 / Total: 9648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.01210069
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg2.6221.78513875
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg2.88451218
ELECTRON MICROSCOPYr_dihedral_angle_2_deg24.32422.148405
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.373151221
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.9131539
ELECTRON MICROSCOPYr_chiral_restr0.1960.21242
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.027995
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.2965.1134881
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it12.8467.6546096
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it5.2624.0715188
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined21.03657.96217410
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.421→3.606 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.49 7959 -
obs--99.95 %

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