[English] 日本語
Yorodumi
- PDB-2y6e: Structure of the D1D2 domain of USP4, the conserved catalytic domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y6e
TitleStructure of the D1D2 domain of USP4, the conserved catalytic domain
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
KeywordsHYDROLASE
Function / homology
Function and homology information


adenosine receptor binding / protein localization to cell surface / TNFR1-induced proapoptotic signaling / protein deubiquitination / spliceosomal tri-snRNP complex assembly / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / regulation of protein stability ...adenosine receptor binding / protein localization to cell surface / TNFR1-induced proapoptotic signaling / protein deubiquitination / spliceosomal tri-snRNP complex assembly / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / regulation of protein stability / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / proteolysis / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLuna-Vargas, M.P.A. / Faesen, A.C. / van Dijk, W.J. / Rape, M. / Fish, A. / Sixma, T.K.
CitationJournal: Nat.Commun. / Year: 2014
Title: The Dusp-Ubl Domain of Usp4 Enhances its Catalytic Efficiency by Promoting Ubiquitin Exchange.
Authors: Clerici, M. / Luna-Vargas, M.P.A. / Faesen, A.C. / Sixma, T.K.
History
DepositionJan 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references / Refinement description / Version format compliance
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Dec 3, 2014Group: Database references / Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
B: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
C: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
D: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
E: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
F: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,45914
Polymers253,8756
Non-polymers5858
Water22,5011249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-180.2 kcal/mol
Surface area85290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.500, 151.030, 178.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 4 / DEUBIQUITINATING ENZYME 4 / UBIQUITIN THIOLESTERASE 4 / ...UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 4 / DEUBIQUITINATING ENZYME 4 / UBIQUITIN THIOLESTERASE 4 / UBIQUITOUS NUCLEAR PROTEIN HOMOLOG / USP4


Mass: 42312.422 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 296-490,765-932
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-NKI-B3C/LIC AND PET46-EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3) PLYSS-T1R / References: UniProt: Q13107, EC: 3.1.2.15
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1249 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM BIS-TRIS PROPANE (PH8.5), 25MM NA2SO4, 18% PEG3350, THEN SOAKED IN 25% ETHYLENEGLYCOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 6, 2009 / Details: MIRRORS
RadiationMonochromator: ASYMMETRIC LAUE 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→44.6 Å / Num. obs: 111095 / % possible obs: 94.9 % / Observed criterion σ(I): 1.1 / Redundancy: 3.4 % / Biso Wilson estimate: 53.38 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 2.4→44.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.4 / % possible all: 74

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GFO

2gfo


Resolution: 2.4→44.59 Å / Cor.coef. Fo:Fc: 0.9415 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 5583 5.03 %RANDOM
Rwork0.178 ---
obs0.1797 111095 --
Displacement parametersBiso mean: 52.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.2468 Å20 Å20 Å2
2---2.383 Å20 Å2
3----1.8638 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15933 0 16 1249 17198
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116348HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0222149HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7421SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes413HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2344HARMONIC5
X-RAY DIFFRACTIONt_it16348HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion6HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion2026SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18154SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2599 329 5.52 %
Rwork0.2205 5636 -
all0.2227 5965 -
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)
12.73420.2956-1.40482.1237-0.0752.5644-0.08590.41790.0142-0.32920.11760.31230.1119-0.4643-0.0317-0.0345-0.0961-0.0989-0.04070.0219-0.106429.451132.239618.1231
21.1187-1.425-1.71380.041.73240.8426-0.0038-0.0209-0.0149-0.0094-0.012-0.04160.01630.03150.01580.0324-0.0044-0.02760.0925-0.07630.013959.620735.336810.7813
33.30620.9004-0.48141.9736-0.58942.69630.0012-0.0752-0.0383-0.0136-0.0106-0.20950.07470.44610.0094-0.0293-0.06010.0022-0.05970.0281-0.127253.184739.006126.3753
40.0365-1.59970.03380.6832-0.59590.3929-0.00340.0196-0.05560.00210.0151-0.01980.0111-0.0098-0.01160.0790.15180.01210.0190.10170.003464.182126.052831.6742
52.67160.978-0.37462.0950.12251.35310.039-0.1090.30830.17320.00930.1773-0.12520.0204-0.0482-0.0028-0.0490.0101-0.1016-0.0038-0.109736.154439.218234.5514
61.83121.1854-0.88162.7330.04822.4195-0.0844-0.0371-0.1221-0.0138-0.0213-0.20340.04880.13080.1057-0.04240.03690.0106-0.07780.0319-0.045216.46678.807548.6998
70.44811.91850.45722.1650.64260.111-0.00510.0024-0.0071-0.0235-0.0064-0.01070.0035-0.01760.01160.0049-0.00170.04360.0154-0.03950.0795-12.0019-4.967250.7162
83.3690.65590.35740.2852-0.02452.3801-0.08350.1569-0.00790.02910.00490.39880.0962-0.37720.0786-0.1681-0.01250.0587-0.043-0.00630.0396-9.62879.772548.2369
90.4871-0.25840.04420.52470.33830.02390.00080.0298-0.0083-0.011-0.0113-0.0250.04050.04230.0105-0.0504-0.15130.06080.0707-0.09730.0666-17.70543.916333.5122
102.54110.5657-0.4312.0547-0.06812.5426-0.0723-0.11590.45610.06980.05170.3698-0.4214-0.37140.0206-0.07150.0920.0236-0.15910.0277-0.03063.372323.044347.9836
112.0926-0.1493-0.13933.71010.40741.4817-0.2133-0.16610.05480.11630.22650.5442-0.1972-0.1505-0.0132-0.1290.0681-0.001-0.11820.13650.056538.6578-0.921448.1993
123.02090.6485-0.90781.0057-0.16272.1191-0.0780.12960.2054-0.06840.0631-0.1983-0.27860.19650.0148-0.0649-0.0497-0.07290.01390.0892-0.030864.23382.116243.4557
130.37522.1385-1.42090-2.29270.5451-0.02450.10370.0106-0.04320.0401-0.0121-0.05230.1145-0.01560.0482-0.02240.0410.09910.062-0.06867.3841-3.991331.125
143.04680.84310.33273.3804-0.70072.736-0.14410.1028-0.15-0.00330.21930.21850.30.2525-0.0752-0.10160.0589-0.0289-0.15260.062-0.096950.7117-15.065743.6953
150.05960.0026-0.08510.0262-0.03360.00210.00240.0037-0.0018-0.0031-0.0020.0015-0.00780.0158-0.00040.0370.0455-0.01890.0201-0.01180.006958.2669-13.883559.8724
162.39050.44590.64242.9772-0.59852.2742-0.12470.3610.1645-0.2086-0.0155-0.20980.06210.12450.1402-0.0536-0.09050.0498-0.06240.0744-0.078323.481-21.356516.6182
170.983-1.5431.05830.2676-0.24450.867-0.00680.0060.00640.0063-0.01620.041-0.02-0.0020.0230.0286-0.0352-0.0250.04110.05750.0315-2.991-24.9177.2859
181.76730.62080.67080.92370.18850-0.0586-0.09040.10830.14580.15530.5442-0.0618-0.2913-0.0967-0.0385-0.07470.083-0.07920.12290.0974-2.3018-28.650524.7924
191.60690.23430.6161.24340.0680.5854-0.0145-0.1483-0.17620.09270.11730.18370.1128-0.1528-0.10280.0371-0.10420.0754-0.09710.0569-0.00749.4884-30.071732.5535
204.04820.88960.4723.9984-0.88910.9451-0.0853-0.021-0.44130.2139-0.127-0.24620.05440.09210.2123-0.0275-0.04980.0214-0.12440.0745-0.020923.7021-31.746931.3203
213.4171.5605-0.93510.84881.51483.39130.02310.14240.15470.04770.1271-0.0428-0.13470.1887-0.1503-0.0244-0.1004-0.08490.00950.054-0.089313.505621.8583-0.5757
222.2345-0.27440.21892.41450.43933.46360.0745-0.24520.1460.20260.092-0.1047-0.00540.0878-0.1665-0.06-0.0872-0.1312-0.01120.0292-0.119911.373919.51768.5558
233.55040.64680.23790.2755-0.37540.8232-0.0191-0.2021-0.19040.03140.05730.26580.2774-0.4919-0.0382-0.1221-0.152-0.11220.12130.1127-0.0784-11.24648.00040.7636
242.25950.3559-1.20161.5645-0.81112.0840.01050.3617-0.1032-0.35140.13520.0870.3901-0.2873-0.1457-0.0563-0.0847-0.1520.05560.0262-0.19297.59428.6835-8.72
250-0.3087-0.21950.1249-0.43730.0059-0.00010.00720.00270.0104-0.0055-0.00290.00950.0250.00560.03540.1164-0.0152-0.02830.08960.0551-10.195723.7277-17.2842
264.3550.5781-0.67422.7917-1.29615.25680.0779-0.2576-0.54420.014-0.04350.00770.1301-0.1487-0.0344-0.1066-0.12130.0121-0.04680.0564-0.139237.8969-11.10872.2091
270.56770.88091.23050.4797-2.71241.98020.0418-0.2982-0.12820.1056-0.1316-0.1216-0.14910.16860.0898-0.0104-0.1520.01880.12740.0326-0.143348.9539-3.5447.5945
285.80961.0834-0.25280.1285-0.03460.9065-0.0336-0.45070.081-0.0801-0.0562-0.306-0.19730.44280.0898-0.1567-0.1520.01470.17560.0556-0.194762.58673.993-2.3889
291.4155-0.72651.33233.6912.03650.3312-0.00790.13460.17880.0962-0.0911-0.0856-0.22270.18820.0990.1286-0.15140.152-0.02460.055-0.178750.11598.8215-7.8193
303.37231.7858-0.01061.1651-2.48854.8901-0.03910.2916-0.0408-0.1850.32550.0215-0.1869-0.2468-0.2864-0.0149-0.06570.03680.01420.0059-0.213638.59760.4911-11.7049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A 297 - A 412 )
2X-RAY DIFFRACTION2(A 413 - A 425 )
3X-RAY DIFFRACTION3(A 426 - A 786 )
4X-RAY DIFFRACTION4(A 787 - A 810 )
5X-RAY DIFFRACTION5(A 811 - A 924 )
6X-RAY DIFFRACTION6(B 296 - B 413 )
7X-RAY DIFFRACTION7(B 414 - B 425 )
8X-RAY DIFFRACTION8(B 426 - B 787 )
9X-RAY DIFFRACTION9(B 788 - B 810 )
10X-RAY DIFFRACTION10(B 811 - B 929 )
11X-RAY DIFFRACTION11(C 296 - C 412 )
12X-RAY DIFFRACTION12(C 413 - C 775 )
13X-RAY DIFFRACTION13(C 776 - C 810 )
14X-RAY DIFFRACTION14(C 811 - C 922 )
15X-RAY DIFFRACTION15(C 923 - C 924 )
16X-RAY DIFFRACTION16(D 297 - D 412 )
17X-RAY DIFFRACTION17(D 413 - D 425 )
18X-RAY DIFFRACTION18(D 426 - D 812 )
19X-RAY DIFFRACTION19(D 813 - D 863 )
20X-RAY DIFFRACTION20(D 864 - D 927 )
21X-RAY DIFFRACTION21(E 297 - E 336 )
22X-RAY DIFFRACTION22(E 337 - E 412 )
23X-RAY DIFFRACTION23(E 413 - E 816 )
24X-RAY DIFFRACTION24(E 817 - E 924 )
25X-RAY DIFFRACTION25(E 925 - E 928 )
26X-RAY DIFFRACTION26(F 296 - F 385 )
27X-RAY DIFFRACTION27(F 386 - F 423 )
28X-RAY DIFFRACTION28(F 424 - F 823 )
29X-RAY DIFFRACTION29(F 824 - F 865 )
30X-RAY DIFFRACTION30(F 866 - F 926 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more