+Open data
-Basic information
Entry | Database: PDB / ID: 4ap4 | ||||||
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Title | Rnf4 - ubch5a - ubiquitin heterotrimeric complex | ||||||
Components |
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Keywords | LIGASE/SIGNALLING PROTEIN / LIGASE-SIGNALLING PROTEIN COMPLEX / CHIMERA | ||||||
Function / homology | Function and homology information regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein polyubiquitination / response to human chorionic gonadotropin / 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 ...regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein polyubiquitination / response to human chorionic gonadotropin / 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 / cellular response to hydroxyurea / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / cellular response to arsenic-containing substance / protein K6-linked ubiquitination / cellular response to testosterone stimulus / Regulation of APC/C activators between G1/S and early anaphase / response to arsenic-containing substance / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / negative regulation of protein localization to chromatin / negative regulation of BMP signaling pathway / nuclear androgen receptor binding / E2 ubiquitin-conjugating enzyme / cellular response to cytokine stimulus / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / Transcriptional Regulation by VENTX / nucleosome binding / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of TORC1 signaling / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TBP-class protein binding / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Plechanovova, A. / Hay, R.T. / Tatham, M.H. / Jaffray, E. / Naismith, J.H. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structure of a Ring E3 Ligase and Ubiquitin-Loaded E2 Primed for Catalysis Authors: Plechanovova, A. / Jaffray, E. / Tatham, M.H. / Naismith, J.H. / Hay, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ap4.cif.gz | 248.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ap4.ent.gz | 200.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ap4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ap4_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 4ap4_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 4ap4_validation.xml.gz | 23 KB | Display | |
Data in CIF | 4ap4_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/4ap4 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4ap4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14758.155 Da / Num. of mol.: 1 / Fragment: RESIDUES 131-195,131-195 Source method: isolated from a genetically manipulated source Details: THE RING DOMAIN IS DUPLICATED BUT AS A FUSED DIMER. THAT IS THE SEQUENCE OF THE RING DOMAIN FROM RNF4 (RESIDUES 131 TO 194) IS LINKED BY A SINGLE GLYCINE RESIDUE TO ANOTHER RING DOMAIN (RESIDUES 131 TO 194). Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O88846, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||||||||
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#2: Protein | Mass: 17134.553 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ISOPEPTIDE AMIDE LINKAGE OF C85K ON UBCH5A TO G76 OF UBIQUITIN CHAIN B LINKED TO CHAIN C (UBIQUITIN) CHAIN E LINKED TO CHAIN F (UBIQUITIN) Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51668, ubiquitin-protein ligase #3: Protein | Mass: 8893.206 Da / Num. of mol.: 2 / Fragment: RESIDUES 76-152 Source method: isolated from a genetically manipulated source Details: ISOPEPTIDE AMIDE LINKED TO UBCH5A (CHAIN B AND CHAIN E) Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: F5H7Y5, UniProt: P0CG48*PLUS #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN B, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN B, CYS 85 TO LYS ...ENGINEERED | Sequence details | THE PROTEIN IS A FUSION DIMER OF TWO MOLECULES OF RNF4. EACH DOMAIN IS SER 131 TO ILE 194. THE N- ...THE PROTEIN IS A FUSION DIMER OF TWO MOLECULES OF RNF4. EACH DOMAIN IS SER 131 TO ILE 194. THE N-TERMINUS HAS A GAMG EXTENSION. GLY 195 LINKS THE TWO SEQUENCES. THUS SER 196 CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 7.2 / Details: pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 31, 2012 / Details: MIRROR |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→190 Å / Num. obs: 32159 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 2.21→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.17 / % possible all: 92 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2YH0 1UBQ 2XEU Resolution: 2.21→94.82 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.981 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.181 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→94.82 Å
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Refine LS restraints |
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