[English] 日本語
Yorodumi- EMDB-44200: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44200 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1 | |||||||||
Map data | Full map from the gold-standard refinement, globally sharpened using an B-factor of -60 A^2, used for model building and refinement. | |||||||||
Sample |
| |||||||||
Keywords | 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 | Function and homology information 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 / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / cell division site / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / modification-dependent protein catabolic process / protein polyubiquitination / protein tag activity / ubiquitin-protein transferase 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 | Schizosaccharomyces pombe 972h- (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Kochanczyk T / Lima CD | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Nature / Year: 2024 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_44200.map.gz | 64.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-44200-v30.xml emd-44200.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44200_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_44200.png | 111.4 KB | ||
Filedesc metadata | emd-44200.cif.gz | 6.7 KB | ||
Others | emd_44200_additional_1.map.gz emd_44200_half_map_1.map.gz emd_44200_half_map_2.map.gz | 63 MB 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44200 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44200 | HTTPS FTP |
-Validation report
Summary document | emd_44200_validation.pdf.gz | 720.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_44200_full_validation.pdf.gz | 720.3 KB | Display | |
Data in XML | emd_44200_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_44200_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44200 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44200 | HTTPS FTP |
-Related structure data
Related structure data | 9b55MC 9b56C 9b57C 9b58C 9b59C 9b5aC 9b5bC 9b5mC 9b5nC 9b5oC 9b5pC 9b5qC 9b5rC 9b5sC 9b5tC 9b5uC 9b5vC 9b5wC 9b5xC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_44200.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full map from the gold-standard refinement, globally sharpened using an B-factor of -60 A^2, used for model building and refinement. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Full map from the gold-standard refinement (unsharpened).
File | emd_44200_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full map from the gold-standard refinement (unsharpened). | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1 from the gold-standard refinement
File | emd_44200_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 from the gold-standard refinement | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2 from the gold-standard refinement
File | emd_44200_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 from the gold-standard refinement | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
Entire | Name: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex |
---|---|
Components |
|
-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 |
---|---|
Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
-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 |
---|---|
Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 17.043336 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
---|---|
Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 8.769948 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
---|---|
Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 44.231828 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
---|---|
Molecular weight | Theoretical: 84.12 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | PDB-9b55: |