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- EMDB-44201: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate ... -
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Open data
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Basic information
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Title | Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 2 | |||||||||
![]() | Full map from the gold-standard refinement, globally sharpened using an B-factor of -40 A^2, used for model building and refinement. | |||||||||
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![]() | UBIQUITIN / E2 / E3 / HECT / NEDD4 / RSP5 / PUB2 / UBC4 / TRANSTHIOESTERIFICATION / THIOESTER / TRANSTHIOLATION / TETRAHEDRAL INTERMEDIATE / ADENYLATION / INHIBITOR / LIGASE / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / UBL / ATP ATP-BINDING / AMP / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND | |||||||||
Function / homology | ![]() RHOQ GTPase cycle / RHOU GTPase cycle / Regulation of PTEN localization / Regulation of PTEN stability and activity / cytoplasm to vacuole targeting by the NVT pathway / cell cortex of cell tip / E3 ubiquitin ligases ubiquitinate target proteins / Peroxisomal protein import / nuclear SCF ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...RHOQ GTPase cycle / RHOU GTPase cycle / Regulation of PTEN localization / Regulation of PTEN stability and activity / cytoplasm to vacuole targeting by the NVT pathway / cell cortex of cell tip / E3 ubiquitin ligases ubiquitinate target proteins / Peroxisomal protein import / nuclear SCF ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / HECT-type E3 ubiquitin transferase / E2 ubiquitin-conjugating enzyme / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cell division site / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / ubiquitin ligase complex / modification-dependent protein catabolic process / protein polyubiquitination / ubiquitin-protein transferase activity / protein tag activity / ubiquitin protein ligase activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleolus / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
![]() | Kochanczyk T / Lima CD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for transthiolation intermediates in the ubiquitin pathway Authors: Kochanczyk T / Hann ZS / Lux MC / Reyes AMVD / Ji C / Tan DS / Lima CD | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 64.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.1 KB 22.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 110 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 62.9 MB 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 770.1 KB | Display | ![]() |
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Full document | ![]() | 769.7 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9b56MC ![]() 9b55C ![]() 9b57C ![]() 9b58C ![]() 9b59C ![]() 9b5aC ![]() 9b5bC ![]() 9b5cC ![]() 9b5dC ![]() 9b5eC ![]() 9b5fC ![]() 9b5gC ![]() 9b5hC ![]() 9b5iC ![]() 9b5jC ![]() 9b5kC ![]() 9b5lC ![]() 9b5mC ![]() 9b5nC ![]() 9b5oC ![]() 9b5pC ![]() 9b5qC ![]() 9b5rC ![]() 9b5sC ![]() 9b5tC ![]() 9b5uC ![]() 9b5vC ![]() 9b5wC ![]() 9b5xC 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 | Full map from the gold-standard refinement, globally sharpened using an B-factor of -40 A^2, used for model building and refinement. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Full map from the gold-standard refinement (unsharpened).
File | emd_44201_additional_1.map | ||||||||||||
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Annotation | Full map from the gold-standard refinement (unsharpened). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 from the gold-standard refinement
File | emd_44201_half_map_1.map | ||||||||||||
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Annotation | Half map 1 from the gold-standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 from the gold-standard refinement
File | emd_44201_half_map_2.map | ||||||||||||
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Annotation | Half map 2 from the gold-standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
Entire | Name: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex |
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Components |
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-Supramolecule #1: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
Supramolecule | Name: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Ubiquitin-conjugating enzyme E2 4
Macromolecule | Name: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 1 Details: C-terminal GGLVPR is a residual artifact after thrombin cleavage of affinity tag Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.043336 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MALKRINREL ADLGKDPPSS SSAGPVGDDL FHWQATIMGP ADSPYAGGVF FLSIHFPTDY PFKPPKVNFT TRIYHPNINS NGSICLDIL RDQWSPALTI SKVLLSISSL LTDPNPDDPL VPEIAHVYKT DRSRYELSAR EWTRKYAIGG LVPR UniProtKB: Ubiquitin-conjugating enzyme E2 4 |
-Macromolecule #2: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 2 Details: N-terminal GSGG is a residual artifact after TEV protease cleavage of affinity tag Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.769948 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRG UniProtKB: Ubiquitin-ribosomal protein eL40B fusion protein |
-Macromolecule #3: E3 ubiquitin-protein ligase pub2
Macromolecule | Name: E3 ubiquitin-protein ligase pub2 / type: protein_or_peptide / ID: 3 Details: N-terminal SHM is a residual artifact after cleaving the affinity tag Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.231828 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SHMDEYQRKI AYMYDRPEMA VNDAQLQLKV SRATTFEDAY DIISKLSVSD MKKKLLIRFR NEDGLDYGGV SREFFYILSH AIFNPGYSL FEYATDDNYG LQISPLSSVN PDFRSYFRFV GRVMGLAIYH RRYLDVQFVL PFYKRILQKP LCLEDVKDVD E VYYESLKW ...String: SHMDEYQRKI AYMYDRPEMA VNDAQLQLKV SRATTFEDAY DIISKLSVSD MKKKLLIRFR NEDGLDYGGV SREFFYILSH AIFNPGYSL FEYATDDNYG LQISPLSSVN PDFRSYFRFV GRVMGLAIYH RRYLDVQFVL PFYKRILQKP LCLEDVKDVD E VYYESLKW IKNNDVDESL CLNFSVEENR FGESVTVDLI PNGRNIAVNN QNKMNYLKAL TEHKLVTSTE EQFNALKGGL NE LIPDSVL QIFNENELDT LLNGKRDIDV QDWKRFTDYR SYTETDDIVI WFWELLSEWS PEKKAKLLQF ATGTSRLPLS GFK DMHGSD GPRKFTIEKV GHISQLPKAH TCFNRLDIPP YNSKEELEQK LTIAIQETAG FGTE UniProtKB: E3 ubiquitin-protein ligase pub2 |
-Macromolecule #4: 4-aminobutanenitrile
Macromolecule | Name: 4-aminobutanenitrile / type: ligand / ID: 4 / Number of copies: 1 / Formula: A1AIV |
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Molecular weight | Theoretical: 84.12 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.5 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
Details: 20 mM Tris-HCl, 100 mM NaCl, 0.1% CHAPSO | ||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 4.0 sec. / Average electron dose: 72.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 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: FLEXIBLE FIT |
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Output model | ![]() PDB-9b56: |