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- EMDB-44217: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model | |||||||||
![]() | Full map from the gold-standard refinement, globally sharpened using an B-factor of -60 A^2, used for model building and refinement. | |||||||||
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![]() | 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 | ![]() 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 / ubiquitin protein ligase binding / DNA damage response / nucleolus / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.79 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 | ![]() | 111.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46.2 KB 46.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.6 KB | Display | ![]() |
Images | ![]() | 138.3 KB | ||
Filedesc metadata | ![]() | 7.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 109 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 108.8 MB 200.4 MB 200.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9b5mMC ![]() 9b55C ![]() 9b56C ![]() 9b57C ![]() 9b58C ![]() 9b59C ![]() 9b5aC ![]() 9b5bC ![]() 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 -60 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).
+Additional map: Full map of Ub(T) 3D class 8 reconstructed...
+Additional map: Full map of Ub(T) 3D class 4 reconstructed...
+Additional map: Full map of Ub(T) 3D class 5 reconstructed...
+Additional map: Full map of Ub(T) 3D class 1 reconstructed...
+Additional map: Full map of Ub(T) 3D class 10 reconstructed...
+Additional map: Full map of Ub(T) 3D class 9 reconstructed...
+Additional map: Full map of Ub(T) 3D class 7 reconstructed...
+Additional map: Full map of Ub(T) 3D class 3 reconstructed...
+Additional map: Full map of Ub(T) 3D class 2 reconstructed...
+Additional map: Full map of Ub(T) 3D class 6 reconstructed...
+Half map: Half map 1 from the gold-standard refinement.
+Half map: Half map 2 from the gold-standard refinement.
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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: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 111.764047 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() |
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 #3: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 3 / 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 #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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.2 Component:
Details: 20 mM Tris-HCl, 100 mM NaCl, 5 mM MgCl2, 1 mM ATP, 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 |
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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-9b5m: |