+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17966 | |||||||||||||||||||||
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Title | Structure of human apo ALDH1A1 determined by cryoEM at 100 keV | |||||||||||||||||||||
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Sample |
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Keywords | Oxidoreductase Aldehyde dehydrogenase / OXIDOREDUCTASE | |||||||||||||||||||||
Function / homology | Function and homology information fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism / Ethanol oxidation / cellular aldehyde metabolic process / RA biosynthesis pathway / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / negative regulation of cold-induced thermogenesis / retinol metabolic process / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y ...McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y / Hutchings KA / Gittins O / Sobhy M / Wells T / El-Gomati MM / Dalby J / Meffert M / Schulze-Briese C / Henderson R / Russo CJ | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structure determination by cryoEM at 100 keV. Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo / Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17966.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-17966-v30.xml emd-17966.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17966_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_17966.png | 100.7 KB | ||
Masks | emd_17966_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-17966.cif.gz | 6.3 KB | ||
Others | emd_17966_half_map_1.map.gz emd_17966_half_map_2.map.gz | 97.2 MB 96.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17966 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17966 | HTTPS FTP |
-Validation report
Summary document | emd_17966_validation.pdf.gz | 745.9 KB | Display | EMDB validaton report |
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Full document | emd_17966_full_validation.pdf.gz | 745.4 KB | Display | |
Data in XML | emd_17966_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_17966_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17966 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17966 | HTTPS FTP |
-Related structure data
Related structure data | 8pvhMC 8pv9C 8pvaC 8pvbC 8pvcC 8pvdC 8pveC 8pvfC 8pvgC 8pviC 8pvjC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17966.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8415 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17966_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17966_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17966_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human apo ALDH1A1
Entire | Name: Human apo ALDH1A1 |
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Components |
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-Supramolecule #1: Human apo ALDH1A1
Supramolecule | Name: Human apo ALDH1A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Aldehyde dehydrogenase 1A1
Macromolecule | Name: Aldehyde dehydrogenase 1A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: aminobutyraldehyde dehydrogenase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.99298 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSYYHHHHHH LESTSLYKKA GSAAAPFTSS SGTPDLPVLL TDLKIQYTKI FINNEWHDSV SGKKFPVFNP ATEEELCQVE EGDKEDVDK AVKAARQAFQ IGSPWRTMDA SERGRLLYKL ADLIERDRLL LATMESMNGG KLYSNAYLND LAGCIKTLRY C AGWADKIQ ...String: MSYYHHHHHH LESTSLYKKA GSAAAPFTSS SGTPDLPVLL TDLKIQYTKI FINNEWHDSV SGKKFPVFNP ATEEELCQVE EGDKEDVDK AVKAARQAFQ IGSPWRTMDA SERGRLLYKL ADLIERDRLL LATMESMNGG KLYSNAYLND LAGCIKTLRY C AGWADKIQ GRTIPIDGNF FTYTRHEPIG VCGQIIPWNF PLVMLIWKIG PALSCGNTVV VKPAEQTPLT ALHVASLIKE AG FPPGVVN IVPGYGPTAG AAISSHMDID KVAFTGSTEV GKLIKEAAGK SNLKRVTLEL GGKSPCIVLA DADLDNAVEF AHH GVFYHQ GQCCIAASRI FVEESIYDEF VRRSVERAKK YILGNPLTPG VTQGPQIDKE QYDKILDLIE SGKKEGAKLE CGGG PWGNK GYFVQPTVFS NVTDEMRIAK EEIFGPVQQI MKFKSLDDVI KRANNTFYGL SAGVFTKDID KAITISSALQ AGTVW VNCY GVVSAQCPFG GFKMSGNGRE LGEYGFHEYT EVKTVTVKIS QKNS UniProtKB: Aldehyde dehydrogenase 1A1 |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: UltrAuFoil R0./1 / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 1400/HR + YPS FEG |
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Image recording | Film or detector model: DECTRIS SINGLA (1k x 1k) / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |