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Yorodumi- EMDB-33354: Cryo-EM structure of empty ring subunit 2 (ER2) from GroEL-UGT1A ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33354 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of empty ring subunit 2 (ER2) from GroEL-UGT1A single empty ring complex | ||||||||||||||||||||||||
Map data | Primary EM-map of GroEL-UGT1A for Subunit ER2 (unmasked) | ||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Escherichia coli (E. coli) / Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||||||||||||||
Authors | Stapleton K / Takagi J / Mizohata E | ||||||||||||||||||||||||
Funding support | Japan, 7 items
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Citation | Journal: To Be Published Title: Unmasking GroEL: Structure, dynamics, and substrate binding revealed by single-particle cryo-EM Authors: Stapleton KM / Mizobata T / Miyazaki N / Takatsuji T / Kato T / Iwasaki K / Standley DM / Kawamura T / Nakane T / Takagi J / Mizohata E | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33354.map.gz | 92.9 MB | EMDB map data format | |
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Header (meta data) | emd-33354-v30.xml emd-33354.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33354_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_33354.png | 125.5 KB | ||
Masks | emd_33354_msk_1.map emd_33354_msk_2.map | 103 MB 103 MB | Mask map | |
Others | emd_33354_additional_1.map.gz emd_33354_half_map_1.map.gz emd_33354_half_map_2.map.gz | 4.3 MB 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33354 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33354 | HTTPS FTP |
-Related structure data
Related structure data | 7xooMC 7xojC 7xokC 7xolC 7xomC 7xonC 7xopC 7xoqC 7xorC 7xosC 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_33354.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Primary EM-map of GroEL-UGT1A for Subunit ER2 (unmasked) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33354_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_33354_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Additional EM-map of a GroEL subunit that was...
File | emd_33354_additional_1.map | ||||||||||||
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Annotation | Additional EM-map of a GroEL subunit that was used for modeling the atomic coordinates (subunit ER2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map-1 used for processing the Primary EM-map of...
File | emd_33354_half_map_1.map | ||||||||||||
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Annotation | Half_map-1 used for processing the Primary EM-map of GroEL-UGT1A for Subunit ER2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map-2 used for processing the Primary EM-map of...
File | emd_33354_half_map_2.map | ||||||||||||
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Annotation | Half_map-2 used for processing the Primary EM-map of GroEL-UGT1A for Subunit ER2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GroEL-UGT1A single empty ring complex
Entire | Name: GroEL-UGT1A single empty ring complex |
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Components |
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-Supramolecule #1: GroEL-UGT1A single empty ring complex
Supramolecule | Name: GroEL-UGT1A single empty ring complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #2: Empty Ring subunit 2 (ER-2) of GroEL
Supramolecule | Name: Empty Ring subunit 2 (ER-2) of GroEL / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: all Details: The model was built in the additional EM-map of ER2 (masked) |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: UDP-glucuronosyltransferase 1A (UGT1A)
Supramolecule | Name: UDP-glucuronosyltransferase 1A (UGT1A) / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Details: Model is not built |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Chaperonin GroEL
Macromolecule | Name: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: chaperonin ATPase |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Molecular weight | Theoretical: 57.260504 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV ...String: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV GKEGVITVED GTGLQDELDV VEGMQFDRGY LSPYFINKPE TGAVELESPF ILLADKKISN IREMLPVLEA VA KAGKPLL IIAEDVEGEA LATLVVNTMR GIVKVAAVKA PGFGDRRKAM LQDIATLTGG TVISEEIGME LEKATLEDLG QAK RVVINK DTTTIIDGVG EEAAIQGRVA QIRQQIEEAT SDYDREKLQE RVAKLAGGVA VIKVGAATEV EMKEKKARVE DALH ATRAA VEEGVVAGGG VALIRVASKL ADLRGQNEDQ NVGIKVALRA MEAPLRQIVL NCGEEPSVVA NTVKGGDGNY GYNAA TEEY GNMIDMGILD PTKVTRSALQ YAASVAGLMI TTECMVTDLP KNDAADLGAA GGMGGMGGMG GMM |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 33 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: Sample containing GorEL-UGT1A was made fresh and used without undergoing any freeze-thaw cycles to avoid degradation in the solution. The sample was in a buffer solution of 150mM NaCl, 20mM Tris-HCl at pH 7.5 | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 3 ul of 33 mg/ml GroEL-UGT1A was placed on Holey carbon Quanitifoil copper grids (300 mesh size R1.2/1.3) and blotted for 3 seconds (blot force =1). |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2951 / Average electron dose: 40.0 e/Å2 Details: Using a Titan KRIOS TEM operated at 300 kV, 2,951 movies were collected using the Falcon III DED in Counting mode at a magnification of 75000x corresponding to a pixel size of 0.87 Pixel/A ...Details: Using a Titan KRIOS TEM operated at 300 kV, 2,951 movies were collected using the Falcon III DED in Counting mode at a magnification of 75000x corresponding to a pixel size of 0.87 Pixel/A at the specimen level. All 2,951 movies were imported into the RELION pipeline and prepared for single-particle analysis |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7xoo: |