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- PDB-5gvi: Zebrafish USP30 in complex with Lys6-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 5gvi
TitleZebrafish USP30 in complex with Lys6-linked diubiquitin
Components
  • (ubiquitin) x 2
  • Ubiquitin carboxyl-terminal hydrolase 30
KeywordsHydrolase/SIGNALING PROTEIN / Complex / mitophagy / Hydrolase-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SCF-beta-TrCP mediated degradation of Emi1 / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 ...Formation of the ternary complex, and subsequently, the 43S complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SCF-beta-TrCP mediated degradation of Emi1 / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / Regulation of pyruvate metabolism / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / E3 ubiquitin ligases ubiquitinate target proteins / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Formation of a pool of free 40S subunits / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / SRP-dependent cotranslational protein targeting to membrane / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of BACH1 activity / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Dual incision in TC-NER / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Oncogene Induced Senescence / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / PINK1-PRKN Mediated Mitophagy / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SCF(Skp2)-mediated degradation of p27/p21 / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 TNFR1 signaling / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity
Similarity search - Function
Cysteine proteinases / Cathepsin B; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...Cysteine proteinases / Cathepsin B; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSato, Y. / Fukai, S.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04750 Japan
Japan Society for the Promotion of Science24687012 Japan
Japan Society for the Promotion of Science15H01175 Japan
Japan Society for the Promotion of Science25112505 Japan
Japan Society for the Promotion of Science25117711 Japan
Japan Society for the Promotion of Science22121003 Japan
Japan Society for the Promotion of Science24247014 Japan
Japan Science and Technology Agency Japan
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30
Authors: Sato, Y. / Okatsu, K. / Saeki, Y. / Yamano, K. / Matsuda, N. / Kaiho, A. / Yamagata, A. / Goto-Ito, S. / Ishikawa, M. / Hashimoto, Y. / Tanaka, K. / Fukai, S.
History
DepositionSep 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _diffrn_detector.detector
Revision 1.2Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 30
B: ubiquitin
C: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3554
Polymers67,2903
Non-polymers651
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-8 kcal/mol
Surface area21480 Å2
Unit cell
Length a, b, c (Å)130.270, 130.270, 59.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 30


Mass: 50492.758 Da / Num. of mol.: 1 / Fragment: UNP residues 61-501 / Mutation: C73A, D127V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: usp30 / Plasmid: pCold-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: A0A0R4ILB8
#2: Protein ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K6R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps27a, Uba80, Ubcep1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62983
#3: Protein ubiquitin


Mass: 8192.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps27a, Uba80, Ubcep1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62983
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 90 mM Tris-HCl, 180 mM ammonium acetate, 23% PEG3350, 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 47938 / % possible obs: 99.6 % / Redundancy: 7.9 % / Net I/σ(I): 42.8
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.38 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I3T

3i3t


Resolution: 1.87→44.083 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 2378 4.96 %
Rwork0.1764 --
obs0.1779 47938 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→44.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 1 123 3904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063848
X-RAY DIFFRACTIONf_angle_d1.0225191
X-RAY DIFFRACTIONf_dihedral_angle_d14.2091447
X-RAY DIFFRACTIONf_chiral_restr0.044586
X-RAY DIFFRACTIONf_plane_restr0.004668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8696-1.90780.30331660.27512631X-RAY DIFFRACTION100
1.9078-1.94930.29591300.25962638X-RAY DIFFRACTION99
1.9493-1.99460.2581230.23892699X-RAY DIFFRACTION99
1.9946-2.04450.2571640.21072616X-RAY DIFFRACTION100
2.0445-2.09980.26691380.20092650X-RAY DIFFRACTION99
2.0998-2.16160.24691570.1982644X-RAY DIFFRACTION100
2.1616-2.23130.20991290.18582682X-RAY DIFFRACTION100
2.2313-2.31110.24061270.17412700X-RAY DIFFRACTION100
2.3111-2.40360.21511530.18142645X-RAY DIFFRACTION100
2.4036-2.5130.2271470.18142697X-RAY DIFFRACTION100
2.513-2.64540.2261250.18382681X-RAY DIFFRACTION100
2.6454-2.81120.21451370.18392699X-RAY DIFFRACTION100
2.8112-3.02820.23731360.19112682X-RAY DIFFRACTION100
3.0282-3.33280.22751420.17752713X-RAY DIFFRACTION100
3.3328-3.81480.19711480.16792676X-RAY DIFFRACTION100
3.8148-4.80540.15661270.14722733X-RAY DIFFRACTION100
4.8054-44.09510.18471290.17322774X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 36.5575 Å / Origin y: 29.4764 Å / Origin z: -0.6696 Å
111213212223313233
T0.2464 Å20.0314 Å2-0.0728 Å2-0.2179 Å20.0034 Å2--0.2043 Å2
L3.0657 °20.9701 °2-0.405 °2-2.5741 °2-0.1344 °2--1.5193 °2
S0.0183 Å °-0.0781 Å °0.2229 Å °0.0521 Å °0.0774 Å °-0.0085 Å °-0.0326 Å °0.0534 Å °-0.058 Å °
Refinement TLS groupSelection details: all

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