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- PDB-8itp: Crystal structure of USP47 catalytic domain complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8itp
TitleCrystal structure of USP47 catalytic domain complex with ubiquitin
Components
  • Ubiquitin
  • Ubiquitin carboxyl-terminal hydrolase 47
KeywordsHYDROLASE/INHIBITOR / Ubiquitin specific protease / HYDROLASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


anterior/posterior axis specification, embryo / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...anterior/posterior axis specification, embryo / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway 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 / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / 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 / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / 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 / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 47, C-terminal / Ubiquitin carboxyl-terminal hydrolase 47 C-terminal / 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 ...Ubiquitin carboxyl-terminal hydrolase 47, C-terminal / Ubiquitin carboxyl-terminal hydrolase 47 C-terminal / 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 / 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 47
Similarity search - Component
Biological speciesHomo sapiens (human)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKim, E.E. / Shin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Commun Biol / Year: 2023
Title: Structural and functional characterization of USP47 reveals a hot spot for inhibitor design.
Authors: Shin, S.C. / Park, J. / Kim, K.H. / Yoon, J.M. / Cho, J. / Ha, B.H. / Oh, Y. / Choo, H. / Song, E.J. / Kim, E.E.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin
D: Ubiquitin carboxyl-terminal hydrolase 47
A: Ubiquitin
B: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4206
Polymers132,2894
Non-polymers1312
Water00
1
C: Ubiquitin
D: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2103
Polymers66,1452
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-7 kcal/mol
Surface area20240 Å2
MethodPISA
2
A: Ubiquitin
B: Ubiquitin carboxyl-terminal hydrolase 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2103
Polymers66,1452
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-8 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.957, 93.399, 217.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
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
#2: Protein Ubiquitin carboxyl-terminal hydrolase 47 / Ubiquitin thioesterase 47 / Ubiquitin-specific-processing protease 47


Mass: 57567.887 Da / Num. of mol.: 2 / Mutation: C97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_T05H10.1, T05H10.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22240, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 1.8 Å3/Da / Density % sol: 31.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
PH range: 4.5 - 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19209 / % possible obs: 96.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.14 / Χ2: 0.915 / Net I/σ(I): 6.6 / Num. measured all: 80505
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.112.80.37417760.842191.4
3.11-3.2330.35118200.862194.4
3.23-3.383.50.31419020.837196.1
3.38-3.563.90.27718800.902197.3
3.56-3.784.20.24619170.988197.7
3.78-4.074.40.18619201.009197.3
4.07-4.484.60.13819401.117197.6
4.48-5.1350.10519640.996197.8
5.13-6.4650.09919970.845198.1
6.46-505.30.06620930.728196.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.20.1-4487refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.51 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 1756 10 %
Rwork0.2461 --
obs0.25 17554 87.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6771 0 2 0 6773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026907
X-RAY DIFFRACTIONf_angle_d0.459325
X-RAY DIFFRACTIONf_dihedral_angle_d12.152583
X-RAY DIFFRACTIONf_chiral_restr0.0371022
X-RAY DIFFRACTIONf_plane_restr0.0041208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.368720.3432646X-RAY DIFFRACTION48
3.08-3.170.387930.3342835X-RAY DIFFRACTION62
3.17-3.280.34621110.34391010X-RAY DIFFRACTION75
3.28-3.390.36631320.30341182X-RAY DIFFRACTION86
3.39-3.530.30131350.30661215X-RAY DIFFRACTION91
3.53-3.690.31451460.28491313X-RAY DIFFRACTION95
3.69-3.880.31271480.25861328X-RAY DIFFRACTION97
3.88-4.120.26911460.2661319X-RAY DIFFRACTION97
4.12-4.440.27771500.2231352X-RAY DIFFRACTION98
4.44-4.890.27411500.20851350X-RAY DIFFRACTION98
4.89-5.590.26721530.2231366X-RAY DIFFRACTION98
5.59-7.030.30711560.24551411X-RAY DIFFRACTION98
7.03-29.510.22291640.2031471X-RAY DIFFRACTION98
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)
16.6787-1.2609-1.3692.2461-1.16686.1940.361-0.2393-0.0604-0.27070.58710.5532-0.0965-0.81280.83560.39580.3523-0.43720.949-0.42210.971758.363210.45134.3313
24.7741-1.313-1.67962.58332.75992.9678-0.03690.35050.2545-0.1619-0.56250.44330.3456-0.34250.3160.77230.43470.19510.9428-0.30010.815758.5805214.768531.4573
32.50011.54321.55823.73850.01211.35290.36490.15661.16380.3533-1.31060.30420.0873-0.01320.86650.9772-0.0062-0.03560.72240.0210.701265.6486224.695536.7133
41.86810.0525-1.18793.3227-0.32941.56380.44230.78430.6343-0.2447-0.44570.9024-0.2004-0.58980.25811.12880.9446-0.24841.0279-0.37650.897854.8941220.004539.1604
55.4466-3.48132.02917.0742-2.33193.24711.08990.14090.54320.0779-0.4349-0.0965-0.0612-1.8081-0.03670.78410.0640.02680.981-0.32761.023153.763215.128245.9021
66.95961.97524.20733.89333.32119.30390.47620.37620.70620.4782-0.189-1.0835-0.4815-0.21790.29630.63910.1484-0.03450.6026-0.08750.67867.9945216.551642.5861
71.35010.8831-2.33244.0993-0.82194.09330.0848-0.2775-0.3861.05190.00520.1611-0.5280.218-0.15330.54580.34080.19611.0785-0.07850.555955.3241209.911847.395
82.00170.34111.13955.8843-1.85074.4773-0.0503-0.5029-0.1942-0.376-1.15980.32420.77170.11890.22980.65070.02410.17540.73960.04130.512857.8219196.87269.6773
93.51292.08091.00495.24232.25865.67840.0044-0.55740.52820.5519-0.4120.1442-0.37510.09290.34970.55920.2652-0.00350.7010.05080.548266.3419204.950870.3723
104.57692.83050.86025.22852.55487.12430.11290.50460.1951-0.8326-0.1418-0.0549-0.26970.50450.20740.54120.09230.00070.63470.18040.439472.6693206.266657.4515
111.0034-0.84260.08741.52980.6512.4438-0.3515-0.002-0.1937-0.0512-0.0033-0.3675-0.0713-0.73280.3590.3315-0.03730.04960.5474-0.11850.536661.6098202.715831.6164
123.77980.54910.44842.07990.65562.054-0.2688-0.4296-0.7865-0.60810.25010.19520.4983-0.80110.15880.5645-0.14120.090.74830.03660.500354.0531194.689946.8377
132.64180.48461.17181.25530.87571.4081-0.2168-0.213-0.51560.44850.2344-0.08880.2041-0.3617-0.1620.61950.00190.27240.52210.11890.624359.57189.618758.9201
142.9028-1.86830.52181.9122-0.37342.789-0.1152-0.035-0.09130.09380.40090.19880.29921.2696-0.5791-0.36760.3324-0.05920.8992-0.18470.49941.8811205.509915.631
151.35910.93460.91840.8074-0.19554.8233-0.5162-0.47720.91380.213-0.19810.3677-1.02810.19710.29710.37-0.0725-0.25380.7083-0.30510.679341.8123210.486515.9797
169.8314-0.30792.97590.7041-1.89215.5611-0.47850.01831.02360.0542-0.36320.1125-0.8429-0.0020.72690.39620.2439-0.18890.4745-0.11740.564534.9257216.35656.2312
175.3163-0.33520.38525.16540.76926.9097-0.4737-0.1450.7618-0.2535-0.6121-0.09370.22181.25791.0530.4983-0.0917-0.08530.31290.28770.635945.4927210.96586.7978
185.58372.52610.03794.626-2.3123.64550.23460.1969-0.1187-0.34140.3422-0.67170.70860.171-0.15250.21020.08720.02070.5879-0.0420.466842.2937201.97214.0309
195.80690.5432-4.33575.3031.95037.14180.54380.5433-0.081-0.19960.30730.32790.0166-0.3856-0.58360.31740.10660.24090.3346-0.14790.62332.024208.20735.7948
204.86850.6041.64762.439-0.41122.5393-0.40371.236-0.7591-0.2398-0.5273-0.9890.18270.60580.11230.43180.0599-0.11790.51340.01060.691744.9545198.42244.8559
211.3999-0.5486-0.40411.68780.7472.6449-0.19450.02460.0114-0.1603-0.06220.15450.14-0.07290.18060.2981-0.04960.01890.29610.06550.322836.2885189.74943.5417
221.7976-0.1751-0.1351.1836-0.26722.4745-0.1899-0.1758-0.36960.16320.0837-0.17970.98020.34440.02990.81140.11690.10760.32250.10650.462543.1958178.14397.4011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'C' and (resid 12 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 17 through 22 )
4X-RAY DIFFRACTION4chain 'C' and (resid 23 through 34 )
5X-RAY DIFFRACTION5chain 'C' and (resid 35 through 44 )
6X-RAY DIFFRACTION6chain 'C' and (resid 45 through 65 )
7X-RAY DIFFRACTION7chain 'C' and (resid 66 through 75 )
8X-RAY DIFFRACTION8chain 'D' and (resid 78 through 106 )
9X-RAY DIFFRACTION9chain 'D' and (resid 107 through 180 )
10X-RAY DIFFRACTION10chain 'D' and (resid 181 through 208 )
11X-RAY DIFFRACTION11chain 'D' and (resid 209 through 288 )
12X-RAY DIFFRACTION12chain 'D' and (resid 289 through 389 )
13X-RAY DIFFRACTION13chain 'D' and (resid 390 through 492 )
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 11 )
15X-RAY DIFFRACTION15chain 'A' and (resid 12 through 16 )
16X-RAY DIFFRACTION16chain 'A' and (resid 17 through 22 )
17X-RAY DIFFRACTION17chain 'A' and (resid 23 through 34 )
18X-RAY DIFFRACTION18chain 'A' and (resid 35 through 49 )
19X-RAY DIFFRACTION19chain 'A' and (resid 50 through 65 )
20X-RAY DIFFRACTION20chain 'A' and (resid 66 through 75 )
21X-RAY DIFFRACTION21chain 'B' and (resid 78 through 298 )
22X-RAY DIFFRACTION22chain 'B' and (resid 299 through 492 )

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