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- PDB-5ohk: Crystal structure of USP30 in covalent complex with ubiquitin pro... -

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Basic information

Entry
Database: PDB / ID: 5ohk
TitleCrystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution)
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30
KeywordsHYDROLASE / Deubiquitinase / DUB / Ubiquitin / USP
Function / homology
Function and homology information


protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / autophagy of mitochondrion / pexophagy / peroxisomal membrane / symbiont entry into host cell via disruption of host cell glycocalyx / mitochondrial fusion / symbiont entry into host cell via disruption of host cell envelope / virus tail ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / autophagy of mitochondrion / pexophagy / peroxisomal membrane / symbiont entry into host cell via disruption of host cell glycocalyx / mitochondrial fusion / symbiont entry into host cell via disruption of host cell envelope / virus tail / negative regulation of mitophagy / protein deubiquitination / Pexophagy / regulation of protein stability / mitochondrial outer membrane / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleus / cytosol
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. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like ...: / 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. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily / Ubiquitin family
Similarity search - Domain/homology
prop-2-en-1-amine / Tail fiber / Ubiquitin carboxyl-terminal hydrolase 30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.3Feb 7, 2024Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,1514
Polymers47,0282
Non-polymers1232
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-6 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.917, 94.408, 96.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30,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: 38469.422 Da / Num. of mol.: 1
Fragment: UNP residues 64-178,UNP residues 217-357,UNP residues 432-502
Mutation: construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, ...Mutation: construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (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-26-82 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 pLacI / Strain (production host): Rosetta 2 (DE3) pLacI / References: UniProt: Q70CQ3, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8558.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLacI / References: UniProt: P0CG47
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2016
RadiationMonochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.34→67.352 Å / Num. obs: 20131 / % possible obs: 99.18 % / Redundancy: 4.2 % / Biso Wilson estimate: 31.81 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.1701 / Rpim(I) all: 0.09162 / Net I/σ(I): 4.61
Reflection shellResolution: 2.34→2.424 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7145 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1978 / CC1/2: 0.848 / Rpim(I) all: 0.3804 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HD5

2hd5


Resolution: 2.34→67.352 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 979 4.88 %Random selection
Rwork0.2291 ---
obs0.2308 20054 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.34→67.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 5 82 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033004
X-RAY DIFFRACTIONf_angle_d0.5254085
X-RAY DIFFRACTIONf_dihedral_angle_d24.3671050
X-RAY DIFFRACTIONf_chiral_restr0.04467
X-RAY DIFFRACTIONf_plane_restr0.003521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3401-2.46350.28331100.2652679X-RAY DIFFRACTION99
2.4635-2.61780.31971540.2592672X-RAY DIFFRACTION99
2.6178-2.820.29471540.25442667X-RAY DIFFRACTION99
2.82-3.10380.24511300.24562683X-RAY DIFFRACTION99
3.1038-3.55290.25351430.23182709X-RAY DIFFRACTION99
3.5529-4.47610.23281220.20032776X-RAY DIFFRACTION99
4.4761-67.3520.25921660.22282889X-RAY DIFFRACTION100

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