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Yorodumi- EMDB-3518: cryo-EM map of the dodecameric F420-reducing hydrogenase Frh at 3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3518 | |||||||||
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Title | cryo-EM map of the dodecameric F420-reducing hydrogenase Frh at 3 Angstrom resolution | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (archaea) / Methanothermobacter marburgensis str. Marburg (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Baerland N / Mills DJ / Vonck J | |||||||||
Citation | Journal: To Be Published Title: cryo-EM map of the dodecameric F420-reducing hydrogenase Frh at 3 Angstrom resolution Authors: Baerland N / Mills DJ / Vonck J | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3518.map.gz | 49.1 MB | EMDB map data format | |
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Header (meta data) | emd-3518-v30.xml emd-3518.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3518_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_3518.png | 293.8 KB | ||
Others | emd_3518_half_map_1.map.gz emd_3518_half_map_2.map.gz | 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3518 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3518 | HTTPS FTP |
-Validation report
Summary document | emd_3518_validation.pdf.gz | 492.1 KB | Display | EMDB validaton report |
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Full document | emd_3518_full_validation.pdf.gz | 491.2 KB | Display | |
Data in XML | emd_3518_validation.xml.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3518 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3518 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3518.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: dodecameric F420-reducing hydrogenase, half map 2
File | emd_3518_half_map_1.map | ||||||||||||
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Annotation | dodecameric F420-reducing hydrogenase, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: dodecameric F420-reducing hydrogenase, half map 1
File | emd_3518_half_map_2.map | ||||||||||||
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Annotation | dodecameric F420-reducing hydrogenase, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : F420 reducing hydrogenase Frh
Entire | Name: F420 reducing hydrogenase Frh |
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Components |
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-Supramolecule #1: F420 reducing hydrogenase Frh
Supramolecule | Name: F420 reducing hydrogenase Frh / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (archaea) |
Molecular weight | Theoretical: 1.2 MDa |
-Macromolecule #1: F420-reducing hydrogenase, subunit alpha
Macromolecule | Name: F420-reducing hydrogenase, subunit alpha / type: protein_or_peptide / ID: 1 / Details: contains a [NiFe] cluster / Enantiomer: LEVO / EC number: coenzyme F420 hydrogenase |
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Source (natural) | Organism: Methanothermobacter marburgensis str. Marburg (archaea) |
Sequence | String: MSERIVISPT SRQEGHAELV MEVDDEGIVT KGRYFSITPV RGLEKMVTGK APETAPVMVQ RICGVCPIP HTLASVEAID DSLDIEVPKA GRLLRELTLA AHHVNSHAIH HFLIAPDFVP E NLMADAIN SVSEIRKNAQ YVVDMVAGEG IHPSDVRIGG MADNITELAR ...String: MSERIVISPT SRQEGHAELV MEVDDEGIVT KGRYFSITPV RGLEKMVTGK APETAPVMVQ RICGVCPIP HTLASVEAID DSLDIEVPKA GRLLRELTLA AHHVNSHAIH HFLIAPDFVP E NLMADAIN SVSEIRKNAQ YVVDMVAGEG IHPSDVRIGG MADNITELAR KRLYARLKQL KP KVNEHVE LMIGLIEDKG LPEGLGVHNQ PTLASHQIYG DRTKFDLDRF TEIMPESWYD DPE IAKRAC STIPLYDGRN VEVGPRARMV EFQGFKERGV VAQHVARALE MKTALSRAIE ILDE LDTSA PVRADFDERG TGKLGIGAIE APRGLDVHMA KVENGKIQFY SALVPTTWNI PTMGP ATEG FHHEYGPHVI RAYDPCLSCA THVMVVDDED KSVIKNEMVK I |
-Macromolecule #2: F420-reducing hydrogenase, subunit beta
Macromolecule | Name: F420-reducing hydrogenase, subunit beta / type: protein_or_peptide / ID: 2 / Details: FrhB contains a [4Fe4S] cluster and an FAD. / Enantiomer: LEVO / EC number: coenzyme F420 hydrogenase |
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Source (natural) | Organism: Methanothermobacter marburgensis str. Marburg (archaea) |
Sequence | String: MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELK AAAGTKYTFS PNVMMLKKAV RQYGIEKLGT VAIPCQTMGI RKMQTYPFGV R FLADKIKL LVGIYCMENF PYTSLQTFIC EKLGVSMELV EKMDIGKGKF ...String: MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELK AAAGTKYTFS PNVMMLKKAV RQYGIEKLGT VAIPCQTMGI RKMQTYPFGV R FLADKIKL LVGIYCMENF PYTSLQTFIC EKLGVSMELV EKMDIGKGKF WVYTQDDVLT LP LKETHGY EQAGCKICKD YVAELADVST GSVGSPDGWS TVITRTDAGD SIFKQAVEAG LFE TKPIEE VKPGLGLLEK LAAQKKEKAE KNIAARKEMG LPTPF |
-Macromolecule #3: F420-reducing hydrogenase, subunit gamma
Macromolecule | Name: F420-reducing hydrogenase, subunit gamma / type: protein_or_peptide / ID: 3 / Details: FrhG contains three [4Fe4S] clusters / Enantiomer: LEVO / EC number: coenzyme F420 hydrogenase |
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Source (natural) | Organism: Methanothermobacter marburgensis str. Marburg (archaea) |
Sequence | String: MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELKA AAGTKYTFSP NVMMLKKAVR QYGIEKLGTV AIPCQTMGIR KMQTYPFGVR FLADKIKLLV GIYCMENFPY TSLQTFICEK LGVSMELVEK MDIGKGKFWV ...String: MVLGTYKEIV SARSTDREIQ KLAQDGGIVT GLLAYALDEG IIEGAVVAGP GEEFWKPQPM VAMSSDELKA AAGTKYTFSP NVMMLKKAVR QYGIEKLGTV AIPCQTMGIR KMQTYPFGVR FLADKIKLLV GIYCMENFPY TSLQTFICEK LGVSMELVEK MDIGKGKFWV YTQDDVLTLP LKETHGYEQA GCKICKDYVA ELADVSTGSV GSPDGWSTVI TRTDAGDSIF KQAVEAGLFE TKPIEEVKPG LGLLEKLAAQ KKEKAEKNIA ARKEMGLPTP F |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||
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Buffer | pH: 7.6 / Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 20 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-10 / Average exposure time: 8.0 sec. / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 45871 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |