+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40465 | |||||||||
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Title | human liver mitochondrial Isovaleryl-CoA dehydrogenase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human / liver / mitochondrial / Isovaleryl-CoA dehydrogenase / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / : / fatty acid beta-oxidation using acyl-CoA dehydrogenase / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix ...isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / : / fatty acid beta-oxidation using acyl-CoA dehydrogenase / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Zhang Z | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell Proteomics / Year: 2023 Title: High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Authors: Zhemin Zhang / Marios L Tringides / Christopher E Morgan / Masaru Miyagi / Jason A Mears / Charles L Hoppel / Edward W Yu / Abstract: The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of ...The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40465.map.gz | 83.3 MB | EMDB map data format | |
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Header (meta data) | emd-40465-v30.xml emd-40465.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40465_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_40465.png | 186.7 KB | ||
Filedesc metadata | emd-40465.cif.gz | 5.1 KB | ||
Others | emd_40465_half_map_1.map.gz emd_40465_half_map_2.map.gz | 154.1 MB 154.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40465 | HTTPS FTP |
-Related structure data
Related structure data | 8sgrMC 8sgpC 8sgsC 8sgvC 8shsC 8sk6C 8sk8C 8skrC 8sksC 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_40465.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8255 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40465_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40465_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Isovaleryl-CoA dehydrogenase
Entire | Name: Isovaleryl-CoA dehydrogenase |
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Components |
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-Supramolecule #1: Isovaleryl-CoA dehydrogenase
Supramolecule | Name: Isovaleryl-CoA dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Isovaleryl-CoA dehydrogenase, mitochondrial
Macromolecule | Name: Isovaleryl-CoA dehydrogenase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: isovaleryl-CoA dehydrogenase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.707703 KDa |
Sequence | String: MAEMATATRL LGWRVASWRL RPPLAGFVSQ RAHSLLPVDD AINGLSEEQR QLRQTMAKFL QEHLAPKAQE IDRSNEFKNL REFWKQLGN LGVLGITAPV QYGGSGLGYL EHVLVMEEIS RASGAVGLSY GAHSNLCINQ LVRNGNEAQK EKYLPKLISG E YIGALAMS ...String: MAEMATATRL LGWRVASWRL RPPLAGFVSQ RAHSLLPVDD AINGLSEEQR QLRQTMAKFL QEHLAPKAQE IDRSNEFKNL REFWKQLGN LGVLGITAPV QYGGSGLGYL EHVLVMEEIS RASGAVGLSY GAHSNLCINQ LVRNGNEAQK EKYLPKLISG E YIGALAMS EPNAGSDVVS MKLKAEKKGN HYILNGNKFW ITNGPDADVL IVYAKTDLAA VPASRGITAF IVEKGMPGFS TS KKLDKLG MRGSNTCELI FEDCKIPAAN ILGHENKGVY VLMSGLDLER LVLAGGPLGL MQAVLDHTIP YLHVREAFGQ KIG HFQLMQ GKMADMYTRL MACRQYVYNV AKACDEGHCT AKDCAGVILY SAECATQVAL DGIQCFGGNG YINDFPMGRF LRDA KLYEI GAGTSEVRRL VIGRAFNADF H UniProtKB: Isovaleryl-CoA dehydrogenase, mitochondrial |
-Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: 35.0 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: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |