+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45001 | |||||||||
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Title | Structure of Mnx H340A complex from Bacillus sp. PL-12 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / multicopper oxidase / manganese biomineralization / METAL TRANSPORT | |||||||||
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. (in: firmicutes) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
Authors | Novikova IV / Evans JE | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45001.map.gz | 68.1 MB | EMDB map data format | |
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Header (meta data) | emd-45001-v30.xml emd-45001.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45001_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_45001.png | 113.4 KB | ||
Masks | emd_45001_msk_1.map | 137.1 MB | Mask map | |
Filedesc metadata | emd-45001.cif.gz | 6.4 KB | ||
Others | emd_45001_half_map_1.map.gz emd_45001_half_map_2.map.gz | 127.4 MB 127.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45001 | HTTPS FTP |
-Validation report
Summary document | emd_45001_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_45001_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_45001_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_45001_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45001 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45001 | HTTPS FTP |
-Related structure data
Related structure data | 9bxaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_45001.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.68 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_45001_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_45001_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_45001_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mnx H340A complex
Entire | Name: Mnx H340A complex |
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Components |
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-Supramolecule #1: Mnx H340A complex
Supramolecule | Name: Mnx H340A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus sp. (in: firmicutes) (bacteria) |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: MnxG
Macromolecule | Name: MnxG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus sp. (in: firmicutes) (bacteria) |
Molecular weight | Theoretical: 138.340672 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MLRKFHVVGI STRIVVNTFG DHNPNGRIYV LKENESKLKD LVRKNPYKPI DLVQPLAIRA NEGDIVEILF ENQLSFSAGM HFQEADYSV LSSDGADAGY NPDTTVEPGG EILYRLNVNQ EGICFFTDLG NVSSTEQGSS VQGLFGALLV QKRGSSWTDP V TGGPINSG ...String: MLRKFHVVGI STRIVVNTFG DHNPNGRIYV LKENESKLKD LVRKNPYKPI DLVQPLAIRA NEGDIVEILF ENQLSFSAGM HFQEADYSV LSSDGADAGY NPDTTVEPGG EILYRLNVNQ EGICFFTDLG NVSSTEQGSS VQGLFGALLV QKRGSSWTDP V TGGPINSG VYADIHHPFL PSFREYAWFF NDEMEIRDLT GERPLNPMTN QEAESFHGVN LRYEPMTNRK RLMEAGVVCP DC DSEEVHH DSWVFGDPAT PILRGYVGDP AVIRLIHGGV KETHVFHYHV HQWLGDSSNI NAEILDAQSI SPQTHYSIQP LYG LGSLHG AIGDSIIHCH LYPAFGIGMW GMNRVFDTLQ DGSQCYPNGV RIKALMPLPD RPEPPKPTPE KPGFPNFIPG KVGY KAPRP PLGIVGGREM TELERNAAIE NPRPGAVFVD PCLDQDPVVV EFNVSAIEMP VVYNKQGWHD PKARFYVMDE DLDDI LSGK KEPEPLVFHV PAGTCIRMNY TNRMPHILDG DAFQLVTRTY ENGFHIHFVK FDVLACDGGN VGWNYDSAVL PGQTIR YEW YAETELKAFF FHDHLFANSH QQHGVFGAGV IQPRFSKFLD SRTGDEVDHG TQISVEHPLI PDYRDQTLFV HDFALLF DK NGRPIQPPEY PGSEDDPGVF GVNFKCEPLK FRLGEDCDPA YSFSSYVHGD PVTPILRAYE GDPIRIRLLQ GAHEESHS F NIHGLRWKEE RPDLGSSMKA QQHIGISESF TFETEIPASG DYLWAFEDEE DVWLGTWGLI RAYKGRMEDL IVLTDREAL PEGSAETPKP TGKPPEKANP LASLPPGAYQ GSPVKKFEVV AFQTPIQYNS YGDHDPYGII FALKEDVEDI LTGKKNPVPL ILRANVGDL VEVTLTSELK KELFPFQDGI HPYPPVKEQS FYPPSLRISL HTSLLNYDVK TSSGDTVGYN PDQTVGPGET I TYRWFVDG QFGMCSMWDM ADLRNHRSFG TFGAFVAESR FTTYLDPYSL EKAITGENVI LRHPLLPATR EFVLILHDGV RL EDKDGKV IIDPMDGVVP DTEELEEVDT YDYGSRGFNY RSERLINRYK EHPVMHELFS SEVFGDPATP LFEAYPGEPV VMR ITTPAE RRRAHTFHLH GHYWKFDSKD LDSRIQSFLG HMVTGHTDDL RLIGGAGGVF NFPGDYLYRS GNIRWDIELG MWGI FRVHK DSKENLPRLE EVEGGWDNEE KA UniProtKB: MnxG |
-Macromolecule #2: MnxE
Macromolecule | Name: MnxE / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus sp. (in: firmicutes) (bacteria) |
Molecular weight | Theoretical: 12.185235 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MHDSPLKSLS AASNVASVND PLFDFFNKHM GKQILIITES SQLNILGQTF RPIFCGKVAE VEPGHLTLSP VTIKILNAPF HKFPIPLSI PFEKIAHFTT DVDCSMRIPL V UniProtKB: MnxE |
-Macromolecule #3: MnxF
Macromolecule | Name: MnxF / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus sp. (in: firmicutes) (bacteria) |
Molecular weight | Theoretical: 12.026734 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MEALFPMSTD YSKMTDVNEI HDSAILEHFR NGIGHKTLVI SPSYPYMFVG IIKELIGDTV MIDVETTHFA QLENREWYIH IHNIEVFYI ERPGAPKIPK LEDY UniProtKB: MnxF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % |
Details | contains 80mM CHAPSO |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |