+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17968 | |||||||||||||||||||||
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Title | Structure of lumazine synthase determined by cryoEM at 100 keV | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | LUMAZINE SYNTHASE / TRANSFERASE | |||||||||||||||||||||
Function / homology | Function and homology information 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Aquifex aeolicus (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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_17968.map.gz | 23 MB | EMDB map data format | |
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Header (meta data) | emd-17968-v30.xml emd-17968.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17968_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_17968.png | 123.6 KB | ||
Masks | emd_17968_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-17968.cif.gz | 6 KB | ||
Others | emd_17968_half_map_1.map.gz emd_17968_half_map_2.map.gz | 98.3 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17968 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17968 | HTTPS FTP |
-Validation report
Summary document | emd_17968_validation.pdf.gz | 962.7 KB | Display | EMDB validaton report |
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Full document | emd_17968_full_validation.pdf.gz | 962.2 KB | Display | |
Data in XML | emd_17968_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_17968_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17968 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17968 | HTTPS FTP |
-Related structure data
Related structure data | 8pvjMC 8pv9C 8pvaC 8pvbC 8pvcC 8pvdC 8pveC 8pvfC 8pvgC 8pvhC 8pviC 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_17968.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: 0.8285 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17968_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17968_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17968_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : lumazine synthase
Entire | Name: lumazine synthase |
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Components |
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-Supramolecule #1: lumazine synthase
Supramolecule | Name: lumazine synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
-Macromolecule #1: 6,7-dimethyl-8-ribityllumazine synthase
Macromolecule | Name: 6,7-dimethyl-8-ribityllumazine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
Molecular weight | Theoretical: 17.76935 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP VAAGELARKE DIDAVIAIGV LIRGATPHF DYIASEVSKG LANLSLELRK PITFGVITAD TLEQAIERAG TKHGNKGWEA ALSAIEMANL FKSLRWSHPQ F EK UniProtKB: 6,7-dimethyl-8-ribityllumazine synthase |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
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: 80.0 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 |