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- PDB-6p9g: Structure of USP5 zinc-finger ubiquitin binding domain co-crystal... -

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Basic information

Entry
Database: PDB / ID: 6p9g
TitleStructure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 2-(4-oxoquinazolin-3(4H)-yl)propanoic acid
ComponentsUbiquitin carboxyl-terminal hydrolase 5
KeywordsPROTEIN BINDING / ubiquitin binding domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


deubiquitinase activity / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome ...deubiquitinase activity / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. ...Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin associated domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2-(4-oxoquinazolin-3(4H)-yl)propanoic acid / Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTempel, W. / Mann, M.K. / Harding, R.J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Schapira, M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain.
Authors: Mann, M.K. / Franzoni, I. / de Freitas, R.F. / Tempel, W. / Houliston, S. / Smith, L. / Vedadi, M. / Arrowsmith, C.H. / Harding, R.J. / Schapira, M.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,81916
Polymers13,5351
Non-polymers28415
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.846, 82.405, 99.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-306-

UNX

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 5 / Deubiquitinating enzyme 5 / Isopeptidase T / Ubiquitin thioesterase 5 / Ubiquitin-specific- ...Deubiquitinating enzyme 5 / Isopeptidase T / Ubiquitin thioesterase 5 / Ubiquitin-specific-processing protease 5


Mass: 13535.199 Da / Num. of mol.: 1 / Fragment: UNP residues 171-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP5, ISOT / Plasmid: pET28-MHL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Codon Plus RIL / References: UniProt: P45974, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-O4Y / (2R)-2-(4-oxoquinazolin-3(4H)-yl)propanoic acid


Mass: 218.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.75 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate, 1.1% v/v dimethyl sulfoxide, 25% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→43.15 Å / Num. obs: 17416 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.074 / Net I/σ(I): 19.7 / Num. measured all: 110415 / Scaling rejects: 2555
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.886.31.791658310380.8590.7881.961.599.2
9.03-43.155.10.0269051770.9980.0130.02968.198

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIMPLE/REFMAC rigid body refinement of coordinates from PDB entry 6DXH

6dxh


Resolution: 2.1→41 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.42 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2477 586 4.9 %
Rwork0.2241 --
obs0.2253 11293 99.86 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.98 Å2 / Biso mean: 38.743 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1--3.4 Å20 Å2-0 Å2
2--7.4 Å20 Å2
3----4 Å2
Refinement stepCycle: final / Resolution: 2.1→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 30 13 936
Biso mean--36.29 34.46 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013932
X-RAY DIFFRACTIONr_bond_other_d0.0010.017799
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6381265
X-RAY DIFFRACTIONr_angle_other_deg1.3561.5781856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0965116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07922.55347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37215143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.092155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 39 -
Rwork0.291 837 -
all-876 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.8996 Å / Origin y: 17.008 Å / Origin z: 17.4558 Å
111213212223313233
T0.1062 Å20.0273 Å2-0.0002 Å2-0.0535 Å2-0.017 Å2--0.1576 Å2
L6.2162 °20.68 °2-0.1094 °2-0.7388 °2-0.2794 °2--4.7025 °2
S-0.0078 Å °0.5042 Å °-0.501 Å °-0.0645 Å °0.0158 Å °-0.0867 Å °0.2421 Å °0.0661 Å °-0.008 Å °

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