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- PDB-9b5l: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9b5l | |||||||||
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Title | Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP) | |||||||||
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![]() | LIGASE / UBIQUITIN / E1 / E2 / UBA1 / UBC4 / TRANSTHIOESTERIFICATION / THIOESTER / TRANSTHIOLATION / TETRAHEDRAL INTERMEDIATE / ADENYLATION / INHIBITOR / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / UBL / ATP ATP-BINDING / AMP / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND | |||||||||
Function / homology | ![]() Hedgehog ligand biogenesis / Regulation of necroptotic cell death / MAPK6/MAPK4 signaling / Josephin domain DUBs / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / ER Quality Control Compartment (ERQC) ...Hedgehog ligand biogenesis / Regulation of necroptotic cell death / MAPK6/MAPK4 signaling / Josephin domain DUBs / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / RAS processing / KEAP1-NFE2L2 pathway / Translesion synthesis by REV1 / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Formation of Incision Complex in GG-NER / Pexophagy / UCH proteinases / Ub-specific processing proteases / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Aggrephagy / Dual Incision in GG-NER / Neddylation / Formation of TC-NER Pre-Incision Complex / Metalloprotease DUBs / Regulation of PTEN localization / Regulation of PTEN stability and activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / enzyme inhibitor activity / E2 ubiquitin-conjugating enzyme / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / ubiquitin ligase complex / meiotic cell cycle / modification-dependent protein catabolic process / protein polyubiquitination / ubiquitin-protein transferase activity / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / proteasome-mediated 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Kochanczyk, T. / Lima, C.D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for transthiolation intermediates in the ubiquitin pathway Authors: Kochanczyk, T. / Hann, Z.S. / Lux, M.C. / Reyes, A.M.V.D. / Ji, C. / Tan, D.S. / Lima, C.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 52.4 KB | Display | |
Data in CIF | ![]() | 77.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44216MC ![]() 9b55C ![]() 9b56C ![]() 9b57C ![]() 9b58C ![]() 9b59C ![]() 9b5aC ![]() 9b5bC ![]() 9b5cC ![]() 9b5dC ![]() 9b5eC ![]() 9b5fC ![]() 9b5gC ![]() 9b5hC ![]() 9b5iC ![]() 9b5jC ![]() 9b5kC ![]() 9b5mC ![]() 9b5nC ![]() 9b5oC ![]() 9b5pC ![]() 9b5qC ![]() 9b5rC ![]() 9b5sC ![]() 9b5tC ![]() 9b5uC ![]() 9b5vC ![]() 9b5wC ![]() 9b5xC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 111764.047 Da / Num. of mol.: 1 / Fragment: residues 13-1012 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: ptr3, SPBC1604.21c, SPBC211.09 / Plasmid: pSMT3 / Production host: ![]() ![]() |
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#2: Protein | Mass: 8568.769 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: ubi4, SPBC337.08c / Plasmid: pET3C / Production host: ![]() ![]() |
#3: Protein | Mass: 17043.336 Da / Num. of mol.: 1 / Mutation: C21S,C107S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: ubc4, SPBC119.02 / Plasmid: pET29b+ / Production host: ![]() ![]() References: UniProt: P46595, E2 ubiquitin-conjugating enzyme |
#4: Protein | Mass: 8769.948 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: uep1, ubi2, SPAC1805.12c / Plasmid: pTXB1 / Production host: ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/AMP.gif)
#5: Chemical | ChemComp-AMP / |
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#6: Chemical | ChemComp-A1AIV / Mass: 84.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2 / Feature type: SUBJECT OF INVESTIGATION |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Covalent E1-Ub-E2 transthiolation intermediate mimic complex with second Ub bound to E1 (doubly Ub-loaded E1-Ub-E2 complex) Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.05% CHAPSO |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12618 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
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