[English] 日本語
Yorodumi- EMDB-44209: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44209 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from consensus | |||||||||
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 / 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: 2.81 Å | |||||||||
Authors | Kochanczyk T / Lima CD | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: To be published 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_44209.map.gz | 111.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-44209-v30.xml emd-44209.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44209_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_44209.png | 139.9 KB | ||
Filedesc metadata | emd-44209.cif.gz | 7.3 KB | ||
Others | emd_44209_additional_1.map.gz emd_44209_additional_2.map.gz emd_44209_half_map_1.map.gz emd_44209_half_map_2.map.gz | 109.1 MB 109 MB 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44209 | HTTPS FTP |
-Validation report
Summary document | emd_44209_validation.pdf.gz | 846.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_44209_full_validation.pdf.gz | 846.3 KB | Display | |
Data in XML | emd_44209_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_44209_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44209 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44209 | HTTPS FTP |
-Related structure data
Related structure data | 9b5eMC 9b5cC 9b5dC 9b5fC 9b5gC 9b5hC 9b5iC 9b5jC 9b5kC 9b5lC 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_44209.map.gz / Format: CCP4 / Size: 216 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 of 3D class reconstructed using particle...
File | emd_44209_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (doubly Ub-loaded - consensus). | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Full map from the gold-standard refinement (unsharpened).
File | emd_44209_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full map from the gold-standard refinement (unsharpened). | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2 from the gold-standard refinement.
File | emd_44209_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 from the gold-standard refinement. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1 from the gold-standard refinement.
File | emd_44209_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 from the gold-standard refinement. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Covalent E1-Ub-E2 transthiolation intermediate mimic complex with...
Entire | Name: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 complex) |
---|---|
Components |
|
-Supramolecule #1: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with...
Supramolecule | Name: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 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-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 |
---|---|
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: Large ribosomal subunit protein eL40B
Macromolecule | Name: Large ribosomal subunit protein eL40B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 8.568769 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Ubiquitin-ribosomal protein eL40B fusion protein |
-Macromolecule #3: Ubiquitin-conjugating enzyme E2 4
Macromolecule | Name: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 3 / 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 #4: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 4 / 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 #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #7: 4-aminobutanenitrile
Macromolecule | Name: 4-aminobutanenitrile / type: ligand / ID: 7 / 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
Buffer | pH: 7.2 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.05% 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-9b5e: |