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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


translation at postsynapse / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 ...translation at postsynapse / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / 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 / Degradation of AXIN / Regulation of TNFR1 signaling / 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 / Deactivation of the beta-catenin transactivating complex / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / Ovarian tumor domain proteases / RAS processing / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2
Similarity search - Function
S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain ...S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
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

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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 / Water


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

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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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