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- PDB-7zc6: Na+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetano... -

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Basic information

Entry
Database: PDB / ID: 7zc6
TitleNa+ - translocating ferredoxin: NAD+ reductase (Rnf) of C. tetanomorphum
Components
  • RnfA
  • RnfB
  • RnfC
  • RnfD
  • RnfE
  • RnfG
KeywordsFLAVOPROTEIN / Rnf / flavin / iron-sulfur cluster / sodium ion translocation / anaerobic energy metabolism / oxidoreductase / electron transport / redox-coupled sodium pump
Function / homology: / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesClostridium tetanomorphum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.27 Å
AuthorsErmler, U. / Vitt, S. / Buckel, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)VI 778/2-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Purification and structural characterization of the Na-translocating ferredoxin: NAD reductase (Rnf) complex of Clostridium tetanomorphum.
Authors: Stella Vitt / Simone Prinz / Martin Eisinger / Ulrich Ermler / Wolfgang Buckel /
Abstract: Various microbial metabolisms use H/Na-translocating ferredoxin:NAD reductase (Rnf) either to exergonically oxidize reduced ferredoxin by NAD for generating a transmembrane electrochemical potential ...Various microbial metabolisms use H/Na-translocating ferredoxin:NAD reductase (Rnf) either to exergonically oxidize reduced ferredoxin by NAD for generating a transmembrane electrochemical potential or reversely to exploit the latter for producing reduced ferredoxin. For cryo-EM structural analysis, we elaborated a quick four-step purification protocol for the Rnf complex from Clostridium tetanomorphum and integrated the homogeneous and active enzyme into a nanodisc. The obtained 4.27 Å density map largely allows chain tracing and redox cofactor identification complemented by biochemical data from entire Rnf and single subunits RnfB, RnfC and RnfG. On this basis, we postulated an electron transfer route between ferredoxin and NAD via eight [4Fe-4S] clusters, one Fe ion and four flavins crossing the cell membrane twice related to the pathway of NADH:ubiquinone reductase. Redox-coupled Na translocation is provided by orchestrating Na uptake/release, electrostatic effects of the assumed membrane-integrated FMN semiquinone anion and accompanied polypeptide rearrangements mediated by different redox steps.
History
DepositionMar 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 23, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / em_software / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_conn / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_atom_id_1 / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_standard_deviation / _pdbx_validate_rmsd_bond.bond_target_value / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_rmsd_bond.linker_flag / _struct_conn.pdbx_dist_value / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Model completeness
Details: The editor has suggested to set the occupancy of the side chains to zero, which are not visible in the 4.2 A map. (I choose "model completeness" as the model was too complete for this ...Details: The editor has suggested to set the occupancy of the side chains to zero, which are not visible in the 4.2 A map. (I choose "model completeness" as the model was too complete for this resolution according to structural experts.)
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RnfA
B: RnfB
C: RnfC
D: RnfD
E: RnfE
G: RnfG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,73818
Polymers169,4756
Non-polymers4,26312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules ABCDEG

#1: Protein RnfA


Mass: 20594.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria)
#2: Protein RnfB


Mass: 28008.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria)
#3: Protein RnfC


Mass: 47164.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria)
#4: Protein RnfD


Mass: 32990.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria)
#5: Protein RnfE


Mass: 21213.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria)
#6: Protein RnfG


Mass: 19502.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Production host: Clostridium tetanomorphum (bacteria)

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Non-polymers , 4 types, 12 molecules

#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Na+ -translocating ferredoxin: NAD+ reductase (Rnf) / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.165 MDa / Experimental value: NO
Source (natural)Organism: Clostridium tetanomorphum (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

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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 / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88423 / Symmetry type: POINT

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