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Yorodumi- PDB-2znv: Crystal structure of human AMSH-LP DUB domain in complex with Lys... -
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-Basic information
Entry | Database: PDB / ID: 2znv | ||||||
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Title | Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer | ||||||
Components |
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Keywords | HYDROLASE/Signaling Protein / protein complex / metal binding protein / Alternative splicing / Hydrolase / Metal-binding / Metalloprotease / Protease / Ubl conjugation pathway / Zinc / Cytoplasm / Nucleus / Phosphoprotein / HYDROLASE-Signaling Protein COMPLEX | ||||||
Function / homology | Function and homology information : / : / Formation of a pool of free 40S subunits / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SRP-dependent cotranslational protein targeting to membrane ...: / : / Formation of a pool of free 40S subunits / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SRP-dependent cotranslational protein targeting to membrane / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Major pathway of rRNA processing in the nucleolus and cytosol / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Termination of translesion DNA synthesis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / Senescence-Associated Secretory Phenotype (SASP) / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Oncogene Induced Senescence / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / L13a-mediated translational silencing of Ceruloplasmin expression / Degradation of AXIN / Regulation of TNFR1 signaling / GTP hydrolysis and joining of the 60S ribosomal subunit / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sato, Y. / Azusa, Y. / Yamagata, A. / Mimura, H. / Wang, X. / Yamashita, M. / Ookata, K. / Nureki, O. / Iwai, K. / Komada, M. / Fukai, S. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains Authors: Sato, Y. / Yoshikawa, A. / Yamagata, A. / Mimura, H. / Yamashita, M. / Ookata, K. / Nureki, O. / Iwai, K. / Komada, M. / Fukai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2znv.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2znv.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 2znv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/2znv ftp://data.pdbj.org/pub/pdb/validation_reports/zn/2znv | HTTPS FTP |
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-Related structure data
Related structure data | 2znrSC 1ubqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 19916.230 Da / Num. of mol.: 2 / Fragment: MPN domain, DUB domain, UNP residues 264-436 / Mutation: E292A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q96FJ0, EC: 3.1.2.15 #2: Protein | Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K63R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62991, UniProt: P0CG50*PLUS #3: Protein | Mass: 8691.918 Da / Num. of mol.: 2 / Mutation: M77D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62991, UniProt: P0CG50*PLUS |
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-Non-polymers , 3 types, 610 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→87.04 Å / Num. all: 83683 / Num. obs: 83683 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.6→1.62 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.2 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2ZNR and 1ubq Resolution: 1.6→32.47 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.629 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The depositors have noticed that 1.7 A is out of range for the link between the GLY76 C atom and the LYS63 NZ atom. However, Refmac5 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The depositors have noticed that 1.7 A is out of range for the link between the GLY76 C atom and the LYS63 NZ atom. However, Refmac5 refined the bond length up to 1.7 A, despite of the declaration of the link record. And, actually, the electron density map shows a little bit longer bonding. So, they concluded that this atypical bonding likely occurs in their structure.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.093 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→32.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.64 Å / Total num. of bins used: 20
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