+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20659 | |||||||||
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Title | Cryo-EM structure of E. coli LonA S679A | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / peptidase activity / cellular response to heat / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity ...endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / peptidase activity / cellular response to heat / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / DNA binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Botos I / Lountos GT / Weimin W / Wlodawer A | |||||||||
Funding support | United States, Russian Federation, 2 items
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Citation | Journal: Curr Res Struct Biol / Year: 2020 Title: Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery Authors: Botos I / Lountos GT / Weimin W / Cherry S / Ghirlando R / Kudzhaev AM / Rotanova TV / de Val N / Tropea J / Gustchina A / Wlodawer A | |||||||||
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_20659.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-20659-v30.xml emd-20659.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_20659.png | 213.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20659 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20659 | HTTPS FTP |
-Validation report
Summary document | emd_20659_validation.pdf.gz | 462 KB | Display | EMDB validaton report |
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Full document | emd_20659_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | emd_20659_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_20659_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20659 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20659 | HTTPS FTP |
-Related structure data
Related structure data | 6u5zMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.848 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ATP-dependent protease La
Entire | Name: ATP-dependent protease La |
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Components |
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-Supramolecule #1: ATP-dependent protease La
Supramolecule | Name: ATP-dependent protease La / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: S679A mutant |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Experimental: 87 KDa |
-Macromolecule #1: Lon protease
Macromolecule | Name: Lon protease / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: endopeptidase La |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 87.546266 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKKI MLVAQKEAST DEPGVNDLFT VGTVASILQM LKLPDGTVK VLVEGLQRAR ISALSDNGEH FSAKAEYLES PTIDEREQEV LVRTAISQFE GYIKLNKKIP PEVLTSLNSI D DPARLADT ...String: MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKKI MLVAQKEAST DEPGVNDLFT VGTVASILQM LKLPDGTVK VLVEGLQRAR ISALSDNGEH FSAKAEYLES PTIDEREQEV LVRTAISQFE GYIKLNKKIP PEVLTSLNSI D DPARLADT IAAHMPLKLA DKQSVLEMSD VNERLEYLMA MMESEIDLLQ VEKRIRNRVK KQMEKSQREY YLNEQMKAIQ KE LGEMDDA PDENEALKRK IDAAKMPKEA KEKAEAELQK LKMMSPMSAE ATVVRGYIDW MVQVPWNARS KVKKDLRQAQ EIL DTDHYG LERVKDRILE YLAVQSRVNK IKGPILCLVG PPGVGKTSLG QSIAKATGRK YVRMALGGVR DEAEIRGHRR TYIG SMPGK LIQKMAKVGV KNPLFLLDEI DKMSSDMRGD PASALLEVLD PEQNVAFSDH YLEVDYDLSD VMFVATSNSM NIPAP LLDR MEVIRLSGYT EDEKLNIAKR HLLPKQIERN ALKKGELTVD DSAIIGIIRY YTREAGVRGL EREISKLCRK AVKQLL LDK SLKHIEINGD NLHDYLGVQR FDYGRADNEN RVGQVTGLAW TEVGGDLLTI ETACVPGKGK LTYTGSLGEV MQESIQA AL TVVRARAEKL GINPDFYEKR DIHVHVPEGA TPKDGPAAGI AMCTALVSCL TGNPVRADVA MTGEITLRGQ VLPIGGLK E KLLAAHRGGI KTVLIPFENK RDLEEIPDNV IADLDIHPVK RIEEVLTLAL QNEPSGMQVV TAK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6u5z: |