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- EMDB-33356: Cryo-EM structure of occupied ring subunit 2 (OR2) of GroEL from ... -
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Open data
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Basic information
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Title | Cryo-EM structure of occupied ring subunit 2 (OR2) of GroEL from GroEL-UGT1A double occupied ring complex | ||||||||||||||||||||||||
![]() | Primary EM-map of OR(2)-GroEL-UGT1A (unmasked) | ||||||||||||||||||||||||
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Function / homology | ![]() GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
![]() | Stapleton K / Takagi J / Mizohata E | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 93.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.5 KB 23.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 120.7 KB | ||
Masks | ![]() ![]() | 103 MB 103 MB | ![]() | |
Others | ![]() ![]() ![]() | 3.4 MB 80.7 MB 80.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xoqMC ![]() 7xojC ![]() 7xokC ![]() 7xolC ![]() 7xomC ![]() 7xonC ![]() 7xooC ![]() 7xopC ![]() 7xorC ![]() 7xosC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Primary EM-map of OR(2)-GroEL-UGT1A (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
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Density Histograms |
-Mask #2
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-Additional map: Additional EM-map of a GroEL subunit that was...
File | emd_33356_additional_1.map | ||||||||||||
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Annotation | Additional EM-map of a GroEL subunit that was used for modeling the atomic coordinates (subunit OR-2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map-2 used for processing the Primary EM-map OR(2)-GroEL-UGT1A
File | emd_33356_half_map_1.map | ||||||||||||
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Annotation | Half_map-2 used for processing the Primary EM-map OR(2)-GroEL-UGT1A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map-1 used for processing the Primary EM-map OR(2)-GroEL-UGT1A
File | emd_33356_half_map_2.map | ||||||||||||
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Annotation | Half_map-1 used for processing the Primary EM-map OR(2)-GroEL-UGT1A | ||||||||||||
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Density Histograms |
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Sample components
-Entire : GroEL-UGT1A double occupied ring complex
Entire | Name: GroEL-UGT1A double occupied ring complex |
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Components |
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-Supramolecule #1: GroEL-UGT1A double occupied ring complex
Supramolecule | Name: GroEL-UGT1A double occupied ring complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: Occupied Ring subunit 2 (OR2) of GroEL
Supramolecule | Name: Occupied Ring subunit 2 (OR2) of GroEL / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: all Details: The model was built in the additional EM-map of OR2-GroEL-UGT1A (masked) |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 57.260504 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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). |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7xoq: |