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- PDB-6h4k: Structure of the Usp25 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6h4k
TitleStructure of the Usp25 C-terminal domain
ComponentsUbiquitin carboxyl-terminal hydrolase 25
KeywordsIMMUNE SYSTEM / Usp / Ubiquitin / Deubiquitinase / Cancer
Function / homology
Function and homology information


ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / protein modification process / regulation of protein stability / peptidase activity ...ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / protein modification process / regulation of protein stability / peptidase activity / ATPase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / ubiquitin protein ligase binding / endoplasmic reticulum / proteolysis / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-like / Ubiquitin interaction motif / Ubiquitin-interacting motif. / 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. ...Ubiquitin carboxyl-terminal hydrolase 14-like / Ubiquitin interaction motif / Ubiquitin-interacting motif. / 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. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / UBA-like superfamily / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1783
Polymers35,1081
Non-polymers712
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-21 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.008, 87.008, 86.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1215-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 25 / Deubiquitinating enzyme 25 / USP on chromosome 21 / Ubiquitin thioesterase 25 / Ubiquitin-specific- ...Deubiquitinating enzyme 25 / USP on chromosome 21 / Ubiquitin thioesterase 25 / Ubiquitin-specific-processing protease 25


Mass: 35107.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP25, USP21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UHP3, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5 22% w/v PEG4000 0.2M SrCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→43.5 Å / Num. obs: 21553 / % possible obs: 100 % / Redundancy: 49.4 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 19.4
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 41 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1608 / CC1/2: 0.512 / Rpim(I) all: 0.759 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→43.504 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 2171 5.44 %
Rwork0.1915 --
obs0.1931 39930 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→43.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 2 57 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012241
X-RAY DIFFRACTIONf_angle_d0.8553028
X-RAY DIFFRACTIONf_dihedral_angle_d15.778844
X-RAY DIFFRACTIONf_chiral_restr0.043334
X-RAY DIFFRACTIONf_plane_restr0.005392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.09460.38931440.3392325X-RAY DIFFRACTION100
2.0946-2.14340.35221270.29692368X-RAY DIFFRACTION100
2.1434-2.1970.29751380.25722386X-RAY DIFFRACTION100
2.197-2.25640.26771910.23772265X-RAY DIFFRACTION100
2.2564-2.32270.23751280.22622390X-RAY DIFFRACTION100
2.3227-2.39770.21561320.21472364X-RAY DIFFRACTION100
2.3977-2.48340.25831350.20692366X-RAY DIFFRACTION100
2.4834-2.58280.24861740.19712305X-RAY DIFFRACTION100
2.5828-2.70040.2519740.19722425X-RAY DIFFRACTION100
2.7004-2.84270.2221240.20232385X-RAY DIFFRACTION100
2.8427-3.02080.26041470.21212340X-RAY DIFFRACTION100
3.0208-3.25390.25271080.2222392X-RAY DIFFRACTION100
3.2539-3.58120.2411680.18382326X-RAY DIFFRACTION100
3.5812-4.09910.23341230.16082386X-RAY DIFFRACTION100
4.0991-5.16310.14461110.14772383X-RAY DIFFRACTION100
5.1631-43.51360.19041470.19562353X-RAY DIFFRACTION100
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)
12.71794.3349-2.29798.1131-1.57696.85020.4801-0.1278-0.92070.57410.0979-0.895-0.56180.58-0.54940.45430.0305-0.01520.6611-0.18180.567154.0792.484131.7917
25.3360.565-2.28573.5168-1.54084.82940.0891-0.1841-0.3024-0.028-0.0561-0.32770.19690.7065-0.06420.3126-0.0181-0.01560.416-0.1160.351540.7873.006330.7274
35.08543.45556.66572.34994.5338.66430.18790.350.24290.1342-0.24420.1128-0.1220.0277-0.1610.4158-0.02550.11610.6654-0.04880.628155.174815.486731.8597
47.7749-0.73485.57094.3263-1.26534.3079-0.56540.81850.4021-0.21430.5052-0.5894-0.47930.1471-0.10030.4642-0.10090.10490.8473-0.12380.923961.65616.49430.1108
54.10870.6819-1.38153.2839-0.41486.40520.2022-0.2930.5522-0.0211-0.1901-0.2016-0.54470.6054-0.21340.3468-0.04010.05350.3527-0.03820.435533.553213.193329.4056
65.4646-0.228-0.9522.31820.70623.06020.08750.04010.11720.0627-0.08090.0354-0.0686-0.1486-0.02590.3037-0.02020.07330.3108-0.05070.32423.9728.809528.6601
73.0043-3.06-1.58023.27331.6022.5694-0.00440.1134-0.95150.2921-0.44110.54980.3116-0.4470.52760.3775-0.11560.0760.4692-0.12860.45259.64485.529732.8754
86.4092-3.1719-2.63795.85132.13298.78920.0985-0.5112-0.27260.3251-0.63230.7057-0.3241-0.68810.26460.4799-0.0337-0.01220.7299-0.24650.7882-0.43617.661935.2155
94.96450.321-1.12912.2436-0.72762.3863-0.14871.8752-0.5188-0.1936-0.2631-0.28431.2449-0.0220.43350.55760.06570.04050.8304-0.22470.612712.58567.595720.1049
107.6703-1.75851.40985.723-1.2563.6081-0.03150.245-0.18390.2236-0.03880.81080.2972-0.98240.10730.3988-0.16780.00090.8116-0.2080.5391-3.1268.677926.5697
114.0599-0.8333-1.63681.1544-0.04680.786-0.0110.53290.5037-0.15160.0041-0.264-0.1026-0.4164-0.06710.51220.0310.03090.4762-0.0120.764718.225717.862525.3763
123.54882.3374-4.93732.7729-4.20828.0491-0.2007-0.0007-0.42830.36890.6383-0.42260.2045-0.1216-0.29830.43750.0454-0.0130.55170.00190.474830.00035.28941.5139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 777 through 793 )
2X-RAY DIFFRACTION2chain 'A' and (resid 794 through 817 )
3X-RAY DIFFRACTION3chain 'A' and (resid 818 through 837 )
4X-RAY DIFFRACTION4chain 'A' and (resid 838 through 860 )
5X-RAY DIFFRACTION5chain 'A' and (resid 861 through 889 )
6X-RAY DIFFRACTION6chain 'A' and (resid 890 through 920 )
7X-RAY DIFFRACTION7chain 'A' and (resid 921 through 945 )
8X-RAY DIFFRACTION8chain 'A' and (resid 946 through 961 )
9X-RAY DIFFRACTION9chain 'A' and (resid 962 through 975 )
10X-RAY DIFFRACTION10chain 'A' and (resid 976 through 1012 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1013 through 1032 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1033 through 1049 )

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