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Yorodumi- EMDB-44227: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44227 | |||||||||
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Title | Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 5 (ATP/Mg) | |||||||||
Map data | Full map from the gold-standard refinement (unsharpened), used for model building and refinement. | |||||||||
Sample |
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Keywords | ubiquitin / E1 / E2 / UBA1 / 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 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 / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...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 / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / modification-dependent protein catabolic process / protein polyubiquitination / protein tag activity / ubiquitin-protein transferase activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / DNA damage response / ubiquitin protein ligase binding / nucleolus / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 Å | |||||||||
Authors | Kochanczyk T / Lima CD | |||||||||
Funding support | United States, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44227.map.gz | 108.1 MB | EMDB map data format | |
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Header (meta data) | emd-44227-v30.xml emd-44227.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44227_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_44227.png | 110.4 KB | ||
Filedesc metadata | emd-44227.cif.gz | 7.2 KB | ||
Others | emd_44227_additional_1.map.gz emd_44227_half_map_1.map.gz emd_44227_half_map_2.map.gz | 108.5 MB 200.5 MB 200.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44227 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44227 | HTTPS FTP |
-Related structure data
Related structure data | 9b5wMC 9b55C 9b56C 9b57C 9b58C 9b59C 9b5aC 9b5bC 9b5mC 9b5nC 9b5oC 9b5pC 9b5qC 9b5rC 9b5sC 9b5tC 9b5uC 9b5vC 9b5xC 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_44227.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Full map from the gold-standard refinement (unsharpened), 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 of 3D class reconstructed using particle...
File | emd_44227_additional_1.map | ||||||||||||
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Annotation | Full map of 3D class reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 from the gold-standard refinement.
File | emd_44227_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_44227_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 |
-Sample components
-Entire : Covalent E1-Ub-E2 transthiolation intermediate mimic complex (sin...
Entire | Name: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (singly Ub-loaded E1-Ub-E2 complex) |
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Components |
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-Supramolecule #1: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (sin...
Supramolecule | Name: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (singly Ub-loaded E1-Ub-E2 complex) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
-Macromolecule #1: Ubiquitin-activating enzyme E1 1
Macromolecule | Name: Ubiquitin-activating enzyme E1 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 111.764047 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SNTIDEGLYS RQLYVLGHEA MKQMSQSNVL IIGCKGLGVE IAKNVCLAGV KSVTLYDPQP TRIEDLSSQY FLTEDDIGVP RAKVTVSKL AELNQYVPVS VVDELSTEYL KNFKCVVVTE TSLTKQLEIN DFTHKNHIAY IAADSRGLFG SIFCDFGENF I CTDTDGNE ...String: SNTIDEGLYS RQLYVLGHEA MKQMSQSNVL IIGCKGLGVE IAKNVCLAGV KSVTLYDPQP TRIEDLSSQY FLTEDDIGVP RAKVTVSKL AELNQYVPVS VVDELSTEYL KNFKCVVVTE TSLTKQLEIN DFTHKNHIAY IAADSRGLFG SIFCDFGENF I CTDTDGNE PLTGMIASIT DDGVVTMLEE TRHGLENGDF VKFTEVKGMP GLNDGTPRKV EVKGPYTFSI GSVKDLGSAG YN GVFTQVK VPTKISFKSL RESLKDPEYV YPDFGKMMRP PQYHIAFQAL SAFADAHEGS LPRPRNDIDA AEFFEFCKKI AST LQFDVE LDEKLIKEIS YQARGDLVAM SAFLGGAVAQ EVLKATTSKF YPLKQYFYFD SLESLPSSVT ISEETCKPRG CRYD GQIAV FGSEFQEKIA SLSTFLVGAG AIGCEMLKNW AMMGVATGES GHISVTDMDS IEKSNLNRQF LFRPRDVGKL KSECA STAV SIMNPSLTGK ITSYQERVGP ESEGIFGDEF FEKLSLVTNA LDNVEARMYV DRRCVFFEKP LLESGTLGTK GNTQVV VPH LTESYGSSQD PPEKSFPICT LKNFPNRIEH TIAWARDLFE GLFKQPIDNV NMYLSSPNFL ETSLKTSSNP REVLENI RD YLVTEKPLSF EECIMWARLQ FDKFFNNNIQ QLLFNFPKDS VTSTGQPFWS GPKRAPTPLS FDIHNREHFD FIVAAASL Y AFNYGLKSET DPAIYERVLA GYNPPPFAPK SGIKIQVNEN EEAPETAANK DKQELKSIAD SLPPPSSLVG FRLTPAEFE KDDDSNHHID FITAASNLRA MNYDITPADR FKTKFVAGKI VPAMCTSTAV VSGLVCLELV KLVDGKKKIE EYKNGFFNLA IGLFTFSDP IASPKMKVNG KEIDKIWDRY NLPDCTLQEL IDYFQKEEGL EVTMLSSGVS LLYANFQPPK KLAERLPLKI S ELVEQITK KKLEPFRKHL VLEICCDDAN GEDVEVPFIC IKL UniProtKB: Ubiquitin-activating enzyme E1 1 |
-Macromolecule #2: Ubiquitin-conjugating enzyme E2 4
Macromolecule | Name: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme |
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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 #3: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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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 #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #6: 4-aminobutanenitrile
Macromolecule | Name: 4-aminobutanenitrile / type: ligand / ID: 6 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.05% CHAPSO |
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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 |
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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: 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 |
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Output model | PDB-9b5w: |