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- PDB-8d1t: Crystal structure of human USP30 in complex with a covalent inhib... -

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Basic information

Entry
Database: PDB / ID: 8d1t
TitleCrystal structure of human USP30 in complex with a covalent inhibitor 552 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. / Cysteine proteinases / Cathepsin B; Chain A ...: / 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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-PXW / Ubiquitin carboxyl-terminal hydrolase 30
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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. / Li, C. / Zhang, K. / Zhang, D. / Hao, Y.
History
DepositionMay 27, 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 13, 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)88,2146
Polymers87,6353
Non-polymers5793
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-32 kcal/mol
Surface area36470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.879, 71.721, 148.630
Angle α, β, γ (deg.)90.000, 93.980, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 , 4 types, 33 molecules

#4: Chemical ChemComp-PXW / (1R,2R,4S,7E)-7-[amino(sulfanyl)methylidene]-2-{[(1P)-3-chloro-3'-(1-cyanocyclopropyl)[1,1'-biphenyl]-4-carbonyl]amino}-7-azabicyclo[2.2.1]heptan-7-ium


Mass: 451.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24ClN4OS / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.5, 22% PEG 4000, 4% 1,3-Butanediol

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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: 2.94→41.78 Å / Num. obs: 18857 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 79.39 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 11
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2985 / % possible all: 98.2

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Processing

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

5ohk

4m43


Resolution: 2.94→40.7 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 917 4.87 %
Rwork0.2361 17920 -
obs0.2391 18837 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.41 Å2 / Biso mean: 92.9642 Å2 / Biso min: 24.39 Å2
Refinement stepCycle: final / Resolution: 2.94→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 35 30 5609
Biso mean--69.7 67.85 -
Num. residues----710
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.94-3.090.34671210.28272502262398
3.09-3.290.39631380.311325432681100
3.29-3.540.34561340.28952536267099
3.54-3.90.31851410.23825382679100
3.9-4.460.26561270.218625682695100
4.46-5.620.29651300.207425852715100
5.62-40.70.24861260.228426482774100

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