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- PDB-5ohp: Crystal structure of USP30 (C77A) in complex with Lys6-linked diu... -

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Basic information

Entry
Database: PDB / ID: 5ohp
TitleCrystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 30
KeywordsHYDROLASE / DUB / Ubiquitin / USP / K6
Function / homology
Function and homology information


protein K6-linked deubiquitination / protein K11-linked deubiquitination / autophagy of mitochondrion / pexophagy / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of mitophagy / protein deubiquitination / female meiosis I / peroxisomal membrane ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / autophagy of mitochondrion / pexophagy / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of mitophagy / protein deubiquitination / female meiosis I / peroxisomal membrane / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / mitochondrial fusion / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / neuron projection morphogenesis / 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 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / 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 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGersch, M. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Mechanism and regulation of the Lys6-selective deubiquitinase USP30.
Authors: Gersch, M. / Gladkova, C. / Schubert, A.F. / Michel, M.A. / Maslen, S. / Komander, D.
History
DepositionJul 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_close_contact ...diffrn_source / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers55,5913
Non-polymers651
Water93752
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-8 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.504, 117.504, 138.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-912-

HOH

21A-926-

HOH

31C-109-

HOH

41C-111-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 30 / Deubiquitinating enzyme 30 / Ubiquitin thioesterase 30 / Ubiquitin-specific-processing protease 30 ...Deubiquitinating enzyme 30 / Ubiquitin thioesterase 30 / Ubiquitin-specific-processing protease 30 / Ub-specific protease 30


Mass: 38437.355 Da / Num. of mol.: 1
Fragment: UNP residues 64-178,UNP residues 217-357,UNP residues 432-502
Mutation: construct 13i (C77A, R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP30 / Plasmid: MG-31-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLacI / References: UniProt: Q70CQ3, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLacI / References: UniProt: P0CG47
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.73 M sodium citrate, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→82.08 Å / Num. obs: 14395 / % possible obs: 99.18 % / Redundancy: 4.7 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1702 / Rpim(I) all: 0.0863 / Net I/σ(I): 6.99
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.9977 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 1402 / CC1/2: 0.713 / Rpim(I) all: 0.5044 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHK

5ohk


Resolution: 2.8→82.077 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 729 5.07 %Random selection
Rwork0.2158 ---
obs0.2176 14379 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→82.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 1 52 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053767
X-RAY DIFFRACTIONf_angle_d0.6955102
X-RAY DIFFRACTIONf_dihedral_angle_d25.0171365
X-RAY DIFFRACTIONf_chiral_restr0.223583
X-RAY DIFFRACTIONf_plane_restr0.004651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-3.01650.34741280.30882686X-RAY DIFFRACTION100
3.0165-3.320.30981530.26212664X-RAY DIFFRACTION100
3.32-3.80050.24711540.22292703X-RAY DIFFRACTION100
3.8005-4.78810.23151480.17782754X-RAY DIFFRACTION100
4.7881-82.1120.21381460.19982843X-RAY DIFFRACTION97

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