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- PDB-2wdt: Crystal structure of Plasmodium falciparum UCHL3 in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wdt | |||||||||
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Title | Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME | |||||||||
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![]() | HYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / ENZYME-LIGAND COMPLEX / UBIQUITIN ISOPEPTIDASE / UCH-L SUPERFAMILY / CYSTEIN PROTEINASE / PEPTIDASE_C12 / HYDROLASE | |||||||||
Function / homology | ![]() 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / 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 / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Weihofen, W.A. / Artavanis-Tsakonas, K. / Gaudet, R. / Ploegh, H.L. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.4 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2we6C ![]() 1xd3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.801, -0.599, 0.008), Vector: |
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Components
#1: Protein | Mass: 26930.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CLONE 3D7 / Plasmid: PET28A / Production host: ![]() ![]() #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.) ![]() ![]() ![]() #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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: BABINET FOR INITIAL AND SIMPLE SCALING FOR FURTHER REFINEMENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.85 Å
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Refine LS restraints |
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