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- PDB-6h4h: Usp28 catalytic domain variant E593D in complex with UbPA -

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Basic information

Entry
Database: PDB / ID: 6h4h
TitleUsp28 catalytic domain variant E593D in complex with UbPA
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE / Ubiquitin / Deubiquitinase / Usp / Cancer
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
prop-2-en-1-amine / Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKlemm, T.A. / Sauer, F. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Mol.Cell / Year: 2019
Title: Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities.
Authors: Sauer, F. / Klemm, T. / Kollampally, R.B. / Tessmer, I. / Nair, R.K. / Popov, N. / Kisker, C.
History
DepositionJul 21, 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 / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
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
Item: _citation.journal_volume / _citation.page_first

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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
B: Ubiquitin carboxyl-terminal hydrolase 28
C: Polyubiquitin-B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,3467
Polymers147,1354
Non-polymers2103
Water0
1
A: Ubiquitin carboxyl-terminal hydrolase 28
C: Polyubiquitin-B
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 28
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,3467
Polymers147,1354
Non-polymers2103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
Buried area8610 Å2
ΔGint-56 kcal/mol
Surface area51760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.745, 213.644, 98.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 65047.879 Da / Num. of mol.: 2 / Mutation: E593D
Source method: isolated from a genetically manipulated source
Details: catalytic domain variant E593D / Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8519.778 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 BL21(DE3) (bacteria) / References: UniProt: P0CG47
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE / Allylamine


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 273 K / Method: vapor diffusion / Details: 0.1 M Citrate pH 5.0 0.8 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.5→49.28 Å / Num. obs: 22722 / % possible obs: 97.8 % / Redundancy: 8.7 % / CC1/2: 0.995 / Rpim(I) all: 0.134 / Net I/σ(I): 7.2
Reflection shellResolution: 3.5→3.78 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4692 / CC1/2: 0.378 / Rpim(I) all: 1.503 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.278 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 33.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 1116 4.92 %Random selection
Rwork0.232 ---
obs0.2344 22697 97.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8365 0 13 0 8378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038557
X-RAY DIFFRACTIONf_angle_d0.76411558
X-RAY DIFFRACTIONf_dihedral_angle_d11.9255160
X-RAY DIFFRACTIONf_chiral_restr0.0461243
X-RAY DIFFRACTIONf_plane_restr0.0051501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.65930.40221400.35332718X-RAY DIFFRACTION100
3.6593-3.85210.32091310.30092692X-RAY DIFFRACTION99
3.8521-4.09340.34321350.26082734X-RAY DIFFRACTION99
4.0934-4.40920.27671500.2362705X-RAY DIFFRACTION99
4.4092-4.85260.26671360.20672665X-RAY DIFFRACTION97
4.8526-5.5540.2961390.2132637X-RAY DIFFRACTION96
5.554-6.99420.32351340.24922626X-RAY DIFFRACTION94
6.9942-49.28290.21241510.18922804X-RAY DIFFRACTION96
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)
11.9081.20830.71993.5183-1.10326.5474-0.26050.7970.3887-0.17540.13860.07920.12590.2457-0.09180.6893-0.081-0.06360.69920.13240.97313.370614.3781-21.3634
26.07530.7828-3.04393.0369-1.55846.3404-0.3333-0.18320.91550.43660.45061.1439-0.3972-0.8053-0.05560.84240.0884-0.14990.79630.25141.05818.268217.774-16.1535
34.4713-1.15180.0141.2312-0.7592.88740.0214-0.89740.00710.7256-0.2379-0.55070.0581-0.4488-0.04751.06890.0138-0.15580.75740.10940.809822.807611.07540.7745
44.0596-1.4386-3.4632.96741.18714.86390.0071-0.58790.60081.70250.23910.4855-0.40990.01120.38191.449-0.0884-0.41330.5485-0.03851.250330.698918.48093.2393
54.27491.26761.03220.75221.28483.57830.8823-0.2469-0.06791.25760.0074-0.8075-0.79261.0091-0.58831.5051-0.3646-0.29070.9463-0.12691.817845.139522.27984.0843
63.57821.9578-3.60413.18840.26389.7194-0.04431.582-0.98580.0084-0.03751.07410.4798-1.54890.27291.4689-0.04860.4151.0907-0.29652.469472.705849.93476.0609
75.61313.91073.02624.5329-0.27753.78081.65710.644-0.82120.1530.3608-2.051-0.13131.1238-0.39431.6823-0.43990.30321.5238-0.75353.121874.045336.75952.4732
84.8381-4.31762.40367.4772-2.63054.18470.0839-0.4287-0.07510.80350.3664-0.7711-0.23591.5110.53521.1261-0.2214-0.42150.35010.32351.406739.022514.7743-7.926
92.73741.11240.7469.07462.81338.5026-0.350.63211.1802-0.13720.4489-0.9362-1.2760.8724-0.29440.8031-0.0810.0120.66160.24211.62629.593924.133-20.1675
102.69270.23121.30873.226-0.17433.9703-0.02560.60270.0858-0.25850.2328-0.63810.29161.1961-0.60211.0163-0.0937-0.2238-0.36620.30931.541827.080212.8734-17.6302
115.7052-4.89344.97725.8011-3.4355.4282-0.29930.4916-0.29150.06761.16290.7867-0.2453-1.4805-0.0380.9053-0.2945-0.18241.96730.39771.22345.99217.4873-38.2793
127.5485-0.2746-1.12583.94031.98415.3414-0.1656-1.4141-0.3146-0.27680.533-0.17020.02191.8339-0.50110.99280.0167-0.01422.9460.17412.290773.565115.8359-30.2644
131.22831.20241.68191.14652.11863.871-0.23580.5933-0.2023-0.36020.1599-0.078-0.3461.50160.21741.0126-0.10030.19862.05080.0311.664253.214418.3203-43.8873
143.2309-0.80660.88325.7413-0.94090.723-0.15060.003-0.3455-0.65130.7671.8913-0.15960.2581-0.17871.1341-0.24190.07581.50380.31521.560123.214235.0381-39.7928
153.2266-1.6583-2.28234.0297-1.26643.8597-0.1433-2.01440.32010.53790.75530.1222-0.61752.78890.38331.0511-0.66860.09832.9483-0.33111.902457.040826.2737-23.2071
167.15962.21913.96911.3458-0.13463.52950.250.6636-1.25670.09350.0306-0.1710.30350.8294-0.02951.0275-0.25140.21982.0562-0.22731.4368.36215.9654-20.7902
174.19823.0412-0.95133.96250.76577.49611.1639-0.93280.80791.9987-0.88751.6195-2.0312-0.5194-0.08132.31570.03720.27051.0754-0.37321.277117.462425.156712.816
188.76546.4923-2.05068.0267-0.29652.77130.5850.14251.88490.7134-0.25591.88920.5252-2.68370.18591.2498-0.0560.02010.94370.09790.892412.188817.14965.5335
194.52022.5049-2.15455.47521.41187.46830.1418-0.53070.19681.34861.0234-0.4916-1.2574-0.90610.12671.24860.0521-0.20240.69140.05390.430418.037519.40947.3101
207.5181-3.7203-3.92858.2953.13662.58131.20070.0971-1.5411-3.0628-1.5744-2.18040.6383-1.60760.34212.81170.13710.34982.53510.21392.299959.433823.4024-60.2969
213.9429-4.8906-0.20948.11262.7152.8979-0.5372-1.56071.0211-0.2899-1.6769-1.2245-0.76310.3731-0.64872.3038-0.80030.37722.62080.63841.896763.596633.0092-56.9447
226.0548-2.696-2.66986.00982.10611.3375-0.98410.26940.8976-2.4468-0.0702-0.3163-0.95092.43830.4561.8213-0.31980.21292.59710.47591.902266.034818.9854-51.0921
233.3463-5.2197-0.71068.34531.90243.44980.251-0.325-0.7251-0.5314-0.1461.8221-0.66682.27481.02591.8706-0.44410.92873.1124-0.00072.534861.556313.3093-59.6024
245.0188-4.4232-3.296.94772.03092.86610.9251-0.92070.9766-0.79570.37140.5226-0.60520.95870.5212.0182-0.0443-0.01083.3220.27972.094757.090122.9145-52.0297
254.8483-5.00431.53225.2165-1.63550.53550.7362-0.76020.64720.5125-0.2005-0.4536-0.2770.971-0.08842.1631-0.2583-0.20552.8382-0.0411.556663.966631.4854-41.5869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 148 through 205 )
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 255 )
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 373 )
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 430 )
6X-RAY DIFFRACTION6chain 'A' and (resid 431 through 534 )
7X-RAY DIFFRACTION7chain 'A' and (resid 535 through 571 )
8X-RAY DIFFRACTION8chain 'A' and (resid 572 through 594 )
9X-RAY DIFFRACTION9chain 'A' and (resid 595 through 634 )
10X-RAY DIFFRACTION10chain 'A' and (resid 635 through 674 )
11X-RAY DIFFRACTION11chain 'A' and (resid 675 through 701 )
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 255 )
13X-RAY DIFFRACTION13chain 'B' and (resid 256 through 398 )
14X-RAY DIFFRACTION14chain 'B' and (resid 399 through 594 )
15X-RAY DIFFRACTION15chain 'B' and (resid 595 through 633 )
16X-RAY DIFFRACTION16chain 'B' and (resid 634 through 697 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 44 )
18X-RAY DIFFRACTION18chain 'C' and (resid 45 through 56 )
19X-RAY DIFFRACTION19chain 'C' and (resid 57 through 75 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 27 )
21X-RAY DIFFRACTION21chain 'D' and (resid 28 through 41 )
22X-RAY DIFFRACTION22chain 'D' and (resid 42 through 55 )
23X-RAY DIFFRACTION23chain 'D' and (resid 56 through 65 )
24X-RAY DIFFRACTION24chain 'D' and (resid 66 through 70 )
25X-RAY DIFFRACTION25chain 'D' and (resid 71 through 75 )

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