+Open data
-Basic information
Entry | Database: PDB / ID: 9bxa | ||||||
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Title | Structure of Mnx H340A complex from Bacillus sp. PL-12 | ||||||
Components |
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Keywords | METAL TRANSPORT / Complex / multicopper oxidase / manganese biomineralization | ||||||
Function / homology | Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / copper ion binding / MnxE / MnxF / MnxG Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
Authors | Novikova, I.V. / Evans, J.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Am Chem Soc / Year: 2024 Title: Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization. Authors: Irina V Novikova / Alexandra V Soldatova / Trevor H Moser / Stephanie M Thibert / Christine A Romano / Mowei Zhou / Bradley M Tebo / James E Evans / Thomas G Spiro / Abstract: The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O directly, via ...The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The β-sheet-rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxEF cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bxa.cif.gz | 379.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bxa.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 9bxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bxa_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9bxa_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9bxa_validation.xml.gz | 59.9 KB | Display | |
Data in CIF | 9bxa_validation.cif.gz | 88.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/9bxa ftp://data.pdbj.org/pub/pdb/validation_reports/bx/9bxa | HTTPS FTP |
-Related structure data
Related structure data | 45001MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 138340.672 Da / Num. of mol.: 1 / Mutation: H340A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (in: firmicutes) (bacteria) Gene: mnxG Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A7KBU7 | ||
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#2: Protein | Mass: 12185.235 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (in: firmicutes) (bacteria) Gene: mnxE Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A7KBU5 #3: Protein | Mass: 12026.734 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (in: firmicutes) (bacteria) Gene: mnxF Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A7KBU6 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mnx H340A complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.21 MDa / Experimental value: YES |
Source (natural) | Organism: Bacillus sp. (in: firmicutes) (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: contains 80mM CHAPSO |
Vitrification | Cryogen name: ETHANE / Humidity: 90 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98663 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 187.03 Å2 | ||||||||||||||||||||||||
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