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- PDB-8d0a: Crystal structure of human USP30 in complex with a covalent inhib... -

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Basic information

Entry
Database: PDB / ID: 8d0a
TitleCrystal structure of human USP30 in complex with a covalent inhibitor 829 and a Fab
Components
  • (mouse anti-huUSP30 Fab ...) x 2
  • Ubiquitin carboxyl-terminal hydrolase 30
KeywordsHYDROLASE / deubiquitinase / covalent inhibitor
Function / homology
Function and homology information


protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / pexophagy / autophagy of mitochondrion / peroxisomal membrane / mitochondrial fusion / negative regulation of mitophagy / protein deubiquitination / Pexophagy ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / pexophagy / autophagy of mitochondrion / peroxisomal membrane / mitochondrial fusion / negative regulation of mitophagy / protein deubiquitination / Pexophagy / regulation of protein stability / ubiquitinyl hydrolase 1 / mitochondrial outer membrane / 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. / Papain-like cysteine peptidase superfamily / Immunoglobulins ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PKH / Ubiquitin carboxyl-terminal hydrolase 30
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsSong, X. / Butler, J. / Li, C. / Zhang, K. / Zhang, D. / Hao, Y.
Funding support2items
OrganizationGrant numberCountry
Other privateAmgen Inc
Other privateCarmot Therapeutics Inc
CitationJournal: To Be Published
Title: TBD
Authors: Song, X. / Butler, J. / Hao, Y.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
H: mouse anti-huUSP30 Fab heavy chain
L: mouse anti-huUSP30 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1295
Polymers87,6353
Non-polymers4942
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-32 kcal/mol
Surface area36430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.229, 71.647, 148.456
Angle α, β, γ (deg.)90, 94.31, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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: 40159.344 Da / Num. of mol.: 1 / Mutation: F348D,M350S,I353E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70CQ3, ubiquitinyl hydrolase 1

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Antibody , 2 types, 2 molecules HL

#2: Antibody mouse anti-huUSP30 Fab heavy chain


Mass: 23822.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody mouse anti-huUSP30 Fab light chain


Mass: 23653.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 21 molecules

#4: Chemical ChemComp-PKH / ~{N}-[(1~{R},2~{R},4~{S},7~{E})-7-[azanyl(sulfanyl)methylidene]-7$l^{4}-azabicyclo[2.2.1]heptan-2-yl]-2-chloranyl-4-(6-cyclopropylpyrazin-2-yl)benzamide


Mass: 428.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 22% PEG 4000, 4% 2,2,2-Trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.19→42.11 Å / Num. obs: 14848 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.6
Reflection shellResolution: 3.19→3.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2656 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHK, 4M43

5ohk

4m43


Resolution: 3.19→42.11 Å / Extinction coef esd: 0.9881 / Cross valid method: THROUGHOUT / σ(F): 1.34
RfactorNum. reflection% reflection
Rfree0.2905 709 4.78 %
Rwork0.2433 --
obs0.2459 14822 98.81 %
Refinement stepCycle: LAST / Resolution: 3.19→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5441 0 29 19 5489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.430.3651390.29812796X-RAY DIFFRACTION99
3.43-3.780.32711270.26572809X-RAY DIFFRACTION98
3.78-4.320.28831340.24572806X-RAY DIFFRACTION99
4.32-5.440.26161470.21432830X-RAY DIFFRACTION99
5.44-42.110.28481620.24212876X-RAY DIFFRACTION99

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