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- PDB-3jyu: Crystal structure of the N-terminal domains of the ubiquitin spec... -

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Basic information

Entry
Database: PDB / ID: 3jyu
TitleCrystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)
ComponentsUbiquitin carboxyl-terminal hydrolase
KeywordsHYDROLASE / Domain in ubiquitin-specific peptidases (DUSP) / proto-oncogene / Ubiquitin-fold / Ubl / protease / thioesterase / Thiol protease / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


adenosine receptor binding / TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Ub-specific processing proteases / protein localization to cell surface / spliceosomal tri-snRNP complex assembly / protein deubiquitination / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling ...adenosine receptor binding / TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Ub-specific processing proteases / protein localization to cell surface / spliceosomal tri-snRNP complex assembly / protein deubiquitination / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / regulation of protein stability / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / : ...DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / : / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Ubiquitin carboxyl-terminal hydrolase 4 / Ubiquitin carboxyl-terminal hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 2.37 Å
AuthorsBacik, J.P. / Avvakumov, G. / Walker, J.R. / Xue, S. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)
Authors: Bacik, J.P. / Avvakumov, G. / Walker, J.R. / Xue, S. / Dhe-Paganon, S.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,1123
Polymers53,9112
Non-polymers2011
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-14 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.060, 34.060, 125.190
Angle α, β, γ (deg.)90.00, 133.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase


Mass: 26955.600 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Usp4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q921M8, UniProt: P35123*PLUS, EC: 3.1.2.15
#2: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1 volume of 9 mg/ml protein solution was mixed with 1 volume of a solution of 20% (w/v) PEG 4000, 10% (v/v) isopropanool, 0.1 M sodium HEPES, and 0.001 M dithiothreitol and equilibrated ...Details: 1 volume of 9 mg/ml protein solution was mixed with 1 volume of a solution of 20% (w/v) PEG 4000, 10% (v/v) isopropanool, 0.1 M sodium HEPES, and 0.001 M dithiothreitol and equilibrated against 1 M NaCl (well solution). The crystal was cryoprotected in well solution mixed 1:1 with a solution containing 60% (v/v) ethylene glycol and 200 mg/ml 3-(1-pyridino)-propene sulfonate (NDSB-201) and frozen by immersion in liquid nitrogen, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2006 / Details: Si(111) double-crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.37→45.4 Å / Num. all: 22820 / Num. obs: 22745 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 39.28 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.104 / Net I/σ(I): 11.9
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3246 / Rsym value: 0.38 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIXmodel building
SHARPphasing
PHENIX(phenix.refine: 1.4_138)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: molecular replacementSAD
Starting model: pdb entry 1W6V

1w6v


Resolution: 2.37→41.227 Å / SU ML: 0.32 / Isotropic thermal model: anisotropic / σ(F): 1.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1110 4.95 %RANDOM
Rwork0.1819 ---
obs0.1844 22421 97.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.845 Å2 / ksol: 0.363 e/Å3
Refinement stepCycle: LAST / Resolution: 2.37→41.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 13 108 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083630
X-RAY DIFFRACTIONf_angle_d1.0624937
X-RAY DIFFRACTIONf_dihedral_angle_d16.6581311
X-RAY DIFFRACTIONf_chiral_restr0.07532
X-RAY DIFFRACTIONf_plane_restr0.004628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.47810.26811450.21022522X-RAY DIFFRACTION94
2.4781-2.60870.26951340.20372662X-RAY DIFFRACTION98
2.6087-2.77210.28081430.19672636X-RAY DIFFRACTION98
2.7721-2.98610.26311390.20292655X-RAY DIFFRACTION99
2.9861-3.28650.26761380.19912684X-RAY DIFFRACTION98
3.2865-3.76180.21931500.17232698X-RAY DIFFRACTION98
3.7618-4.73830.19291250.14442721X-RAY DIFFRACTION98
4.7383-41.23280.19751360.15882733X-RAY DIFFRACTION95
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)
10.51920.29430.09950.25770.27810.5593-0.8288-0.5228-0.297-0.5307-0.50540.07630.2417-0.5865-0.01410.21120.08030.05860.45330.01740.34936.053411.255914.4761
20.17960.01170.27850.10220.05740.2931-0.10410.23610.4074-0.0224-0.0378-0.1697-0.3519-0.0108-0.00070.16260.0329-0.08560.1281-0.03820.353350.082918.119712.3507
30.7080.153-0.2927-0.03520.08080.45440.2112-0.32110.15170.1843-0.08680.02330.5134-0.08570.0040.18940.04020.01860.1176-0.05750.247956.57599.045319.397
41.168-0.49360.45771.2225-0.14610.751-0.2087-0.78110.2567-0.22720.18010.38650.1256-0.39250.00510.2872-0.00070.0144-0.1033-0.00480.245845.492110.08560.4766
50.75710.8150.10350.8886-0.09330.05570.3516-0.4816-0.38110.00570.00420.03950.1984-0.15070.00030.2896-0.001-0.05170.13390.03880.279551.264-3.516.5026
61.38070.74971.3450.80270.01722.560.1614-0.3328-0.12490.3003-0.0527-0.04310.1595-0.16270.00010.24240.0296-0.01950.10320.01610.230752.30495.292418.4987
70.18010.06520.13130.0480.04580.0689-0.2524-0.3167-0.222-0.54580.1398-0.3751-0.02380.5080.00050.2163-0.0102-0.03160.3062-0.07380.450171.867912.125523.466
80.261-0.0916-0.18640.02370.05350.11460.2452-0.3319-0.0474-0.1164-0.7785-0.00880.30090.19410.00030.3652-0.0065-0.11460.25730.03280.283268.4049-2.274130.4406
90.4833-0.6799-0.32760.8750.4310.20760.449-0.1386-0.4273-0.0121-0.00320.46040.2301-0.1009-0.00060.4609-0.1318-0.18770.55190.07150.371871.2846-2.747440.2474
100.65420.1152-0.02110.7072-0.63790.53980.21420.14140.6534-0.02350.20520.00290.707-0.5472-0.00010.4893-0.0125-0.09670.54630.14440.339774.03910.104148.4273
110.08710.11760.0070.11680.01050.00870.88531.04810.0235-0.56890.4802-0.3514-0.4630.7935-0.00430.90330.04-0.06610.643-0.27990.645685.1988-7.666935.6603
121.3347-0.41780.76650.1145-0.25270.3760.1376-0.13-0.1019-0.2402-0.11190.31030.34960.407-0.00010.441-0.0202-0.01860.42750.08450.235779.5674-0.65742.1064
130.12950.1663-0.18130.5690.08290.4793-0.2124-0.23920.61020.1905-0.03010.0947-0.66880.17120.00020.30330.0639-0.05680.3317-0.13280.342989.749218.767522.9419
140.48230.3690.38550.25850.35130.4388-0.0582-0.1930.39670.2398-0.0187-0.00770.10640.1578-00.1885-0.00870.06780.26440.02520.241381.313810.902812.762
150.4735-0.12930.45390.4304-0.34210.4840.3756-0.12970.20820.5443-0.28190.01580.0611-0.1481-0.00010.3130.01250.07860.3737-0.07050.213190.84912.213531.1719
160.82520.2736-0.25540.26480.12120.2776-0.13050.6205-0.24170.22730.29590.03290.4010.73420.00030.30310.0819-0.00890.2282-0.12190.20689.779-0.197112.8458
170.4708-0.3183-0.16790.4327-0.20430.399-0.0873-0.2303-0.22190.29420.40170.01670.1799-0.3165-0.00010.2856-0.0220.01620.29110.00150.259577.38762.375214.8967
180.2595-0.08970.30410.0121-0.06660.3937-0.00590.52560.203-0.034-0.14070.0646-0.14160.67780.00030.20230.0396-0.00250.3179-0.04760.221490.963610.602711.3895
190.0287-0.0284-0.00820.13-0.03-0.03110.30430.5433-0.1012-0.1427-0.15290.27980.1202-0.26250.00010.2614-0.0363-0.02440.21860.05850.375868.033411.2417.8378
200.71020.40920.10211.0896-0.53260.4089-0.17790.2357-0.215-0.18280.0523-0.24280.005-0.41420.00010.2733-0.120.05660.51320.03170.249773.00860.206-11.5765
210.08940.01480.01860.103-0.16460.2685-0.32890.0481-0.2526-0.34410.65710.4528-0.09230.48390.00040.1914-0.0231-0.01140.52770.10810.278369.29129.3482-11.0127
221.0383-0.2983-0.03390.0613-0.06190.22630.06030.31760.4757-0.34050.18510.53420.1034-0.35140.00070.2357-0.1365-0.02180.68210.10320.229366.36252.4273-18.0786
230.47570.3857-0.06960.78890.0420.1169-0.2131-0.3876-0.526-0.6019-0.01180.58160.1176-0.7716-0.00080.13-0.06890.1270.72320.07440.347660.34384.9451-8.1613
240.7199-0.5746-0.23361.93470.8930.4308-0.10810.6002-0.3571-0.18760.21920.0003-0.2149-0.9710.00160.3383-0.316-0.06431.01670.16280.230364.9461.1555-19.7898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 9:14
2X-RAY DIFFRACTION2chain A and resid 15:30
3X-RAY DIFFRACTION3chain A and resid 31:44
4X-RAY DIFFRACTION4chain A and resid 45:64
5X-RAY DIFFRACTION5chain A and resid 65:87
6X-RAY DIFFRACTION6chain A and resid 88:122
7X-RAY DIFFRACTION7chain A and resid 123:136
8X-RAY DIFFRACTION8chain A and resid 137:144
9X-RAY DIFFRACTION9chain A and resid 145:168
10X-RAY DIFFRACTION10chain A and resid 169:187
11X-RAY DIFFRACTION11chain A and resid 188:196
12X-RAY DIFFRACTION12chain A and resid 197:228
13X-RAY DIFFRACTION13chain B and resid 12:29
14X-RAY DIFFRACTION14chain B and resid 30:44
15X-RAY DIFFRACTION15chain B and resid 45:64
16X-RAY DIFFRACTION16chain B and resid 65:85
17X-RAY DIFFRACTION17chain B and resid 86:98
18X-RAY DIFFRACTION18chain B and resid 99:121
19X-RAY DIFFRACTION19chain B and resid 122:139
20X-RAY DIFFRACTION20chain B and resid 140:161
21X-RAY DIFFRACTION21chain B and resid 162:171
22X-RAY DIFFRACTION22chain B and resid 172:193
23X-RAY DIFFRACTION23chain B and resid 194:209
24X-RAY DIFFRACTION24chain B and resid 210:228

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