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Yorodumi- PDB-5lbn: High-resolution crystal structure of the UBC core domain of UBE2E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lbn | ||||||
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Title | High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6 | ||||||
Components | Ubiquitin-conjugating enzyme E2 E1 | ||||||
Keywords | TRANSFERASE / UBC core / Ubiquitination / E2 Ubiquitin-conjugating enzyme | ||||||
Function / homology | Function and homology information ISG15 transferase activity / ISG15-protein conjugation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...ISG15 transferase activity / ISG15-protein conjugation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ISG15 antiviral mechanism / CDK-mediated phosphorylation and removal of Cdc6 / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein ubiquitination / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Anandapadamanaban, M. / Moche, M. / Sunnerhagen, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: To Be Published Title: Structure of a TRIM21 - UBE2E1 complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGs Authors: Anandapadamanaban, M. / Moche, M. / Sunnerhagen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lbn.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lbn.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/5lbn ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lbn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17619.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E1, UBCH6 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Ros-2 References: UniProt: P51965, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium citrate pH 6 and 8% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.282416 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282416 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→37.06 Å / Num. obs: 26209 / % possible obs: 94.8 % / Redundancy: 11.568 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 33.21 |
Reflection shell | Resolution: 1.42→1.51 Å / Redundancy: 9.66 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 13.15 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→37.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.99 Å2 / Biso mean: 17.7812 Å2 / Biso min: 8.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→37.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.419→1.456 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.786 Å / Origin y: 4.237 Å / Origin z: 9.416 Å
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