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- PDB-6hei: Structure of the catalytic domain of USP28 (insertion deleted) bo... -

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Basic information

Entry
Database: PDB / ID: 6hei
TitleStructure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE / Ubiquitin / USP / Ubiquitin-specific protease / DUB / Deubiquitinase / protease / isopeptidase / USP28
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / response to ionizing radiation / female gonad development / seminiferous tubule development ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / response to ionizing radiation / female gonad development / seminiferous tubule development / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / DNA damage checkpoint signaling / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD
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. / UBA-like superfamily / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. ...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. / UBA-like superfamily / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGersch, M. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council724804 United Kingdom
CitationJournal: Mol.Cell / Year: 2019
Title: Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity.
Authors: Gersch, M. / Wagstaff, J.L. / Toms, A.V. / Graves, B. / Freund, S.M.V. / Komander, D.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 15, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3623
Polymers53,3002
Non-polymers621
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomeric behaviour was observed by SAXS and SEC-MALS analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-4 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.505, 86.414, 97.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28


Mass: 44586.691 Da / Num. of mol.: 1
Mutation: residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS,residues 400-579 replaced by GSGSGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLacI / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8713.023 Da / Num. of mol.: 1 / Mutation: residue 76 replaced with PA warhead
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 276 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22% (w/v) PEG 3350, 300 mM potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.64→49.51 Å / Num. obs: 52145 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Net I/σ(I): 13.5
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5114 / CC1/2: 0.69 / Rrim(I) all: 0.733 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NBF

1nbf


Resolution: 1.64→49.51 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.71
RfactorNum. reflection% reflection
Rfree0.2138 2574 4.94 %
Rwork0.1857 --
obs0.1871 52144 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 4 276 3679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073499
X-RAY DIFFRACTIONf_angle_d0.9974741
X-RAY DIFFRACTIONf_dihedral_angle_d23.8161277
X-RAY DIFFRACTIONf_chiral_restr0.329502
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.67150.26311370.25762681X-RAY DIFFRACTION99
1.6715-1.70570.31021570.25532713X-RAY DIFFRACTION100
1.7057-1.74280.25961640.2322698X-RAY DIFFRACTION100
1.7428-1.78330.27271350.22422729X-RAY DIFFRACTION100
1.7833-1.82790.25531460.21022710X-RAY DIFFRACTION100
1.8279-1.87730.26251220.20872732X-RAY DIFFRACTION100
1.8773-1.93260.23081160.19922723X-RAY DIFFRACTION100
1.9326-1.9950.25321350.20232757X-RAY DIFFRACTION100
1.995-2.06630.23171440.19642738X-RAY DIFFRACTION100
2.0663-2.1490.23471300.19362739X-RAY DIFFRACTION100
2.149-2.24680.2491420.1832736X-RAY DIFFRACTION100
2.2468-2.36530.20021530.17942743X-RAY DIFFRACTION100
2.3653-2.51350.21331550.18592730X-RAY DIFFRACTION100
2.5135-2.70750.24311570.18242748X-RAY DIFFRACTION100
2.7075-2.980.20261410.18342795X-RAY DIFFRACTION100
2.98-3.41120.19971650.17362773X-RAY DIFFRACTION100
3.4112-4.29760.18641310.16222839X-RAY DIFFRACTION100
4.2976-64.8230.19041440.18782986X-RAY DIFFRACTION100

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