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Yorodumi- PDB-2l00: Solution structure of the non-covalent complex of the ZNF216 A20 ... -
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-Basic information
Entry | Database: PDB / ID: 2l00 | ||||||
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Title | Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/PEPTIDE BINDING PROTEIN / A20 domain / ZNF216 / ubiquitin / zinc finger / ubiquitin binding / METAL BINDING PROTEIN-PEPTIDE BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information : / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling ...: / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / : / UCH proteinases / Regulation of PTEN stability and activity / Aggrephagy / Regulation of TP53 Degradation / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translesion synthesis by POLK / Translesion synthesis by POLI / Peroxisomal protein import / Orc1 removal from chromatin / Translesion synthesis by REV1 / ABC-family proteins mediated transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Endosomal Sorting Complex Required For Transport (ESCRT) / respiratory system process / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / smooth muscle tissue development / fibroblast migration / vasculature development / skeletal system morphogenesis / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Formation of TC-NER Pre-Incision Complex / Ub-specific processing proteases / Dual incision in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / face development / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / platelet-derived growth factor receptor signaling pathway / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / ribosomal large subunit assembly / protein tag activity / ribosome biogenesis / cytoplasmic translation / cytosolic large ribosomal subunit / in utero embryonic development / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / Rigid Body Docking, molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Garner, T.P. / Long, J.E. / Searle, M.S. / Layfield, R. | ||||||
Citation | Journal: To be Published Title: Co-localisation of ubiquitin receptors ZNF216 and p62 in a ubiquitin-mediated ternary complex Authors: Garner, T.P. / Strachan, J. / Long, J.E. / Layfield, R. / Searle, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l00.cif.gz | 330.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l00.ent.gz | 272.6 KB | Display | PDB format |
PDBx/mmJSON format | 2l00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/2l00 ftp://data.pdbj.org/pub/pdb/validation_reports/l0/2l00 | HTTPS FTP |
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-Related structure data
Related structure data | 2kzyC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6538.265 Da / Num. of mol.: 1 / Fragment: A20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: rCG_48158, Zfand5, Zfp216_predicted / Production host: Escherichia coli (E. coli) / Strain (production host): c41 (DE3) / References: UniProt: B5DF11 |
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#2: Protein | Mass: 8568.769 Da / Num. of mol.: 1 / Fragment: ubiquitin core domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PUBI-2, UBI1 / Production host: Escherichia coli (E. coli) / Strain (production host): c41 (DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR derived solution structure of the A20 zinc finger of ZNF216 with ubiquitin derived from NOE, PRE and RDC measurements | ||||||||||||||||||||||||||||||||||||||||||||
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-Sample preparation
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