+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15851 | |||||||||
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Title | Cryo-EM structure of cytochrome bd oxidase from C. glutamicum | |||||||||
Map data | RELION masked postprocessing map | |||||||||
Sample |
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Function / homology | Function and homology information cytochrome complex / aerobic electron transport chain / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Corynebacterium glutamicum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||
Authors | Grund TN / Kusumoto T / Michel H / Sakamoto J / Safarian S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To be published Title: Cryo-EM structure of cytochrome bd oxidase from C. glutamicum Authors: Grund TN / Michel H / Safarian S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15851.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-15851-v30.xml emd-15851.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15851_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_15851.png | 59.9 KB | ||
Masks | emd_15851_msk_1.map | 64 MB | Mask map | |
Others | emd_15851_additional_1.map.gz emd_15851_half_map_1.map.gz emd_15851_half_map_2.map.gz | 49.3 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15851 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15851 | HTTPS FTP |
-Validation report
Summary document | emd_15851_validation.pdf.gz | 705.5 KB | Display | EMDB validaton report |
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Full document | emd_15851_full_validation.pdf.gz | 705.1 KB | Display | |
Data in XML | emd_15851_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | emd_15851_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15851 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15851 | HTTPS FTP |
-Related structure data
Related structure data | 8b4oMC 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_15851.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | RELION masked postprocessing map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15851_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: RELION masked 3D refinement map
File | emd_15851_additional_1.map | ||||||||||||
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Annotation | RELION masked 3D refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION 3D refinement half map 1
File | emd_15851_half_map_1.map | ||||||||||||
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Annotation | RELION 3D refinement half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION 3D refinement half map 2
File | emd_15851_half_map_2.map | ||||||||||||
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Annotation | RELION 3D refinement half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CydAB heterodimer
Entire | Name: CydAB heterodimer |
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Components |
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-Supramolecule #1: CydAB heterodimer
Supramolecule | Name: CydAB heterodimer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Corynebacterium glutamicum (bacteria) |
Molecular weight | Theoretical: 93 KDa |
-Macromolecule #1: Cytochrome bd-type quinol oxidase subunit II
Macromolecule | Name: Cytochrome bd-type quinol oxidase subunit II / type: protein_or_peptide / ID: 1 / Details: cydB / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Corynebacterium glutamicum (bacteria) |
Molecular weight | Theoretical: 36.261582 KDa |
Recombinant expression | Organism: Corynebacterium glutamicum (bacteria) |
Sequence | String: MDHNTFWFIL IAFLFSGYFL LEGFDFGVGI LAPIIGKDSA ARNTVIRTIG PVWDGNEVWL IVAGGALFAA FPEWYATMFS GMYLPLFLV LVSLIIRVVG LEWRKKVDDP RWQKWSDRAI FIGSWTPPLM WGFIFANILR GMPIKADHTI DAAAALPGMV N VFAILGAL ...String: MDHNTFWFIL IAFLFSGYFL LEGFDFGVGI LAPIIGKDSA ARNTVIRTIG PVWDGNEVWL IVAGGALFAA FPEWYATMFS GMYLPLFLV LVSLIIRVVG LEWRKKVDDP RWQKWSDRAI FIGSWTPPLM WGFIFANILR GMPIKADHTI DAAAALPGMV N VFAILGAL AFTALFALHG LAFIRLKTAG RVRTDAAKAA PGVALLAAVT GGPFVLWAAI AYGRSWSWIL AVLIIAAVLG GA FALIKDR DGLSFLSTSV AVIGVVALLF SSLFPNVMPT TLADGVSLDI WNASASHYAL TILTWTAAVI APLVVLYQGW TYW VFRKRL HAEPVSA |
-Macromolecule #2: Cytochrome BD ubiquinol oxidase subunit I
Macromolecule | Name: Cytochrome BD ubiquinol oxidase subunit I / type: protein_or_peptide / ID: 2 / Details: CydA / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Corynebacterium glutamicum (bacteria) |
Molecular weight | Theoretical: 56.678461 KDa |
Recombinant expression | Organism: Corynebacterium glutamicum (bacteria) |
Sequence | String: MDVVDIARWQ FGITTVYHFI FVPLTIGLAP LVAIMQTFWQ VTGKEHWYRA TRFFGTVLLI NFAVGVATGI VQEFQFGMNW SEYSRFVGD VFGGPLALEG LIAFFLESVF LGLWIFGWGK IPGWLHTASI WIVAIATNIS AYFIIVANSF MQHPVGAEYN P ETGRAELT ...String: MDVVDIARWQ FGITTVYHFI FVPLTIGLAP LVAIMQTFWQ VTGKEHWYRA TRFFGTVLLI NFAVGVATGI VQEFQFGMNW SEYSRFVGD VFGGPLALEG LIAFFLESVF LGLWIFGWGK IPGWLHTASI WIVAIATNIS AYFIIVANSF MQHPVGAEYN P ETGRAELT DFWALLTNST ALAAFPHAVA GGFLTAGTFV LGISGWWIIR AHRQAKKAEA EIESKHSMHR PALWVGWWTT VV SSVALFI TGDTQAKLMF VQQPMKMASA ESLCETATDP NFSILTIGTH NNCDTVTHLI DVPFVLPFLA EGKFTGVTLQ GVN QLQAAA EQAYGPGNYS PNLFVTYWSF RAMIGLMLGS LAIAAIAWLL LRKKRTPTGK IARLFQIGSL IAIPFPFLAN SAGW IFTEM GRQPWVVHPN PESAGDARTE MIRMTVDMGV SDHAPWQVWL TLIGFTILYL ILFVVWVWLI RRAVLIGPPE EGAPS VEAK TGPATPIGSD MPMTPLQFTA AAPTTREKE |
-Macromolecule #3: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
Macromolecule | Name: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 3 / Number of copies: 1 / Formula: HDD |
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Molecular weight | Theoretical: 632.487 Da |
Chemical component information | ChemComp-HDD: |
-Macromolecule #4: HEME B/C
Macromolecule | Name: HEME B/C / type: ligand / ID: 4 / Number of copies: 2 / Formula: HEB |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ChemComp-HEB: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 107.0 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: 2.1 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |