[English] 日本語
Yorodumi- PDB-2wdt: Crystal structure of Plasmodium falciparum UCHL3 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wdt | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / ENZYME-LIGAND COMPLEX / UBIQUITIN ISOPEPTIDASE / UCH-L SUPERFAMILY / CYSTEIN PROTEINASE / PEPTIDASE_C12 / HYDROLASE | |||||||||
Function / homology | Function and homology information Synthesis of active ubiquitin: roles of E1 and E2 enzymes / UCH proteinases / Neddylation / : / : / deNEDDylase activity / protein modification process => GO:0036211 / protein deneddylation / protein deubiquitination / Peptide chain elongation ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / UCH proteinases / Neddylation / : / : / deNEDDylase activity / protein modification process => GO:0036211 / protein deneddylation / protein deubiquitination / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / cytosolic ribosome / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling Similarity search - Function | |||||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Weihofen, W.A. / Artavanis-Tsakonas, K. / Gaudet, R. / Ploegh, H.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Characterization and Structural Studies of the Plasmodium Falciparum Ubiquitin and Nedd8 Hydrolase Uchl3. Authors: Artavanis-Tsakonas, K. / Weihofen, W.A. / Antos, J.M. / Coleman, B.I. / Comeaux, C.A. / Duraisingh, M.T. / Gaudet, R. / Ploegh, H.L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wdt.cif.gz | 133 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wdt.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wdt ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wdt | HTTPS FTP |
---|
-Related structure data
Related structure data | 2we6C 1xd3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.801, -0.599, 0.008), Vector: |
-Components
#1: Protein | Mass: 26930.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: CLONE 3D7 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IKM8*PLUS, ubiquitinyl hydrolase 1 #2: Protein | Mass: 8618.910 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-75 Source method: isolated from a genetically manipulated source Details: C-TERMINAL GLY76 OF WILDTYPE UBIQUITIN IS REPLACED BY A VINYL METHYLESTER MOIETY (UBVME) Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | METHYL 4-AMINOBUTANOATE (GVE): ACTIVE SITE CYS95 OF UCHL3 FORMS A COVALENT BOND TO METHYL 4- ...METHYL 4-AMINOBUTAN | Sequence details | CDNA OF PLASMODIUM FALCIPARUM UCHL3 WAS GENERATED AS DESCRIBED IN FRICKEL ET AL., CELL. MICROBIOL. ...CDNA OF PLASMODIUM | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 / Details: 100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 30, 2007 Details: TRIPLE STRIPED VERTICAL AND HORIZANTAL FOCUSSING MIRRORS IN KIRKPATRICK- BAEZ GEOMETRY |
Radiation | Monochromator: CRYOGENICALLY-COOLED DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 39592 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 90.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XD3 Resolution: 2.3→19.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.763 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-4 AND 227-232 OF CHAINS A AND C ARE DISORDERED RESTRAINTS FOR REFMAC5 FOR METHYL 4- AMINOBUTANOATE WERE GENERATED WITH THE DUNDEE PRODRG DSERVER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å Solvent model: BABINET FOR INITIAL AND SIMPLE SCALING FOR FURTHER REFINEMENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.33 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|