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- PDB-9f6g: Human USP30 chimera bound to Ubiquitin-PA -

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Basic information

Entry
Database: PDB / ID: 9f6g
TitleHuman USP30 chimera bound to Ubiquitin-PA
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35
KeywordsHYDROLASE / USP30 / Ubiquitin / DUB / deubiquitinating enzyme / USP14 / USP35 / mitophagy / USP / Ubiquitin-specific protease / Ubiquitin carboxyl-terminal hydrolase 30 / Ubiquitin-PA / Ub-PA
Function / homology
Function and homology information


protein K6-linked deubiquitination / protein K11-linked deubiquitination / negative regulation of ERAD pathway / regulation of chemotaxis / protein K48-linked deubiquitination / deubiquitinase activity / autophagy of mitochondrion / pexophagy / peroxisomal membrane / symbiont entry into host cell via disruption of host cell glycocalyx ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / negative regulation of ERAD pathway / regulation of chemotaxis / protein K48-linked deubiquitination / deubiquitinase activity / autophagy of mitochondrion / pexophagy / peroxisomal membrane / symbiont entry into host cell via disruption of host cell glycocalyx / mitochondrial fusion / endopeptidase inhibitor activity / K63-linked deubiquitinase activity / symbiont entry into host cell via disruption of host cell envelope / virus tail / negative regulation of mitophagy / proteasome binding / negative regulation of ubiquitin-dependent protein catabolic process / protein deubiquitination / regulation of proteasomal protein catabolic process / presynaptic cytosol / Pexophagy / Regulation of NF-kappa B signaling / proteasome complex / regulation of protein stability / cytoplasmic vesicle / chemical synaptic transmission / mitochondrial outer membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / innate immune response / cysteine-type endopeptidase activity / nucleolus / glutamatergic synapse / cell surface / endoplasmic reticulum / mitochondrion / proteolysis / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain / Ubiquitin carboxyl-terminal hydrolase 14-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 carboxyl-terminal hydrolase 38-like, N-terminal domain / Ubiquitin carboxyl-terminal hydrolase 14-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 domain signature. / Ubiquitin conserved site / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Tail fiber / Ubiquitin carboxyl-terminal hydrolase 14 / Ubiquitin carboxyl-terminal hydrolase 30 / Ubiquitin carboxyl-terminal hydrolase 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKazi, N.H. / Gersch, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck SocietyCGCIII-352S Germany
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30.
Authors: Kazi, N.H. / Klink, N. / Gallant, K. / Kipka, G.M. / Gersch, M.
History
DepositionMay 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7043
Polymers44,6462
Non-polymers571
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-7 kcal/mol
Surface area15670 Å2
Unit cell
Length a, b, c (Å)46.639, 50.706, 156.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35 / 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 / Deubiquitinating enzyme 14 / Ubiquitin thioesterase 14 / Ubiquitin-specific-processing protease 14 / Deubiquitinating enzyme 35 / Ubiquitin thioesterase 35 / Ubiquitin-specific-processing protease 35


Mass: 36126.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP30, USP14, TGT, USP35, KIAA1372, USP34 / Production host: Escherichia coli (E. coli)
References: UniProt: Q70CQ3, UniProt: P54578, UniProt: Q9P2H5, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8519.778 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) / References: UniProt: P0CG47
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.56 M sodium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→46.64 Å / Num. obs: 58606 / % possible obs: 97.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2821 / CC1/2: 0.426 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS3.19.0-g3823b7bec-releasedata reduction
xia23.18.0data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
Coot0.9.8.93model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.7 Å / SU ML: 0.1572 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 2888 4.94 %
Rwork0.183 55579 -
obs0.1843 58467 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 4 355 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412825
X-RAY DIFFRACTIONf_angle_d1.33053831
X-RAY DIFFRACTIONf_chiral_restr0.0885445
X-RAY DIFFRACTIONf_plane_restr0.0126488
X-RAY DIFFRACTIONf_dihedral_angle_d14.26241017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.27061580.25842548X-RAY DIFFRACTION96.54
1.52-1.550.2771370.25082600X-RAY DIFFRACTION96.07
1.55-1.580.27421470.24052572X-RAY DIFFRACTION96.45
1.58-1.610.28251450.2332618X-RAY DIFFRACTION96.78
1.61-1.640.26041330.22642623X-RAY DIFFRACTION96.74
1.64-1.680.24131520.21992586X-RAY DIFFRACTION96.75
1.68-1.720.23841470.22352629X-RAY DIFFRACTION97.34
1.72-1.760.27751190.20972617X-RAY DIFFRACTION97.06
1.76-1.810.23231250.21382662X-RAY DIFFRACTION96.87
1.81-1.860.21741480.19082677X-RAY DIFFRACTION98.4
1.86-1.920.2621260.17982647X-RAY DIFFRACTION98.12
1.92-1.990.1931290.17292664X-RAY DIFFRACTION97.83
1.99-2.070.25011290.18492681X-RAY DIFFRACTION98.25
2.07-2.160.20181420.1822693X-RAY DIFFRACTION98.37
2.16-2.280.18971510.17632669X-RAY DIFFRACTION97.98
2.28-2.420.22761310.18282457X-RAY DIFFRACTION89.64
2.42-2.610.19411300.17962319X-RAY DIFFRACTION84.56
2.61-2.870.20541280.18442765X-RAY DIFFRACTION99.04
2.87-3.280.21911460.18062767X-RAY DIFFRACTION99.49
3.28-4.140.16521320.15282816X-RAY DIFFRACTION99.63
4.14-44.70.20231330.18082969X-RAY DIFFRACTION99.2
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9401143448850.02507245892080.384669978481.007015630490.2382259164951.91731508282-0.03840694203080.1381738498370.0478958502092-0.05751961650390.134145301308-0.0714139684184-0.1139714220760.228145671977-0.08340145470540.133126695797-0.03959867113850.01333261991250.118663947963-0.01417892851820.1571368383786.92353567602-1.2002566625322.6617131822
22.04753929874-0.5026562095220.8798226279842.55184166822-1.22281793045.09185090725-0.07014182381010.24138139810.221572685064-0.2418124797230.01397590039020.228576800349-0.505530763557-0.2988313746490.03420257523020.2061612551830.00436946212396-0.02553533160670.1739616879070.01732909676790.189589722554-8.976131377382.5741211248911.7835724051
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 66 through 502)AA66 - 5021 - 281
22(chain 'B' and resid 1 through 76)BB - C1 - 761

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