[English] 日本語
Yorodumi
- PDB-4a3p: Structure of USP15 DUSP-UBL deletion mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a3p
TitleStructure of USP15 DUSP-UBL deletion mutant
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of antifungal innate immune response / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling ...negative regulation of antifungal innate immune response / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / SMAD binding / protein deubiquitination / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / 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. / Ubiquitin carboxyl-terminal hydrolase, C-terminal ...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 carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / 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) / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IODIDE ION / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsElliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L.
CitationJournal: FEBS Lett. / Year: 2011
Title: Structural Variability of the Ubiquitin Specific Protease Dusp-Ubl Double Domains.
Authors: Elliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L.
History
DepositionOct 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _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 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3303
Polymers25,1441
Non-polymers1862
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.950, 44.250, 56.150
Angle α, β, γ (deg.)90.00, 104.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15 / DEUBIQUITINATING ENZYME 15 / UBIQUITIN THIOLESTERASE 15 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15 ...DEUBIQUITINATING ENZYME 15 / UBIQUITIN THIOLESTERASE 15 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15 / UNPH-2 / UNPH4 / USP15


Mass: 25144.334 Da / Num. of mol.: 1 / Fragment: DUSP-UBL, RESIDUES 6-123,127-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 124-126 (VKH) WERE SUB-CLONED OUT OF THE SEQUENCE TO GENERATE A DELETION MUTANT. F123 IS ...RESIDUES 124-126 (VKH) WERE SUB-CLONED OUT OF THE SEQUENCE TO GENERATE A DELETION MUTANT. F123 IS PEPTIDE LINKED TO C127.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.7 % / Description: NONE
Crystal growpH: 7 / Details: 1.9 M (NH4)2SO4, 100 MM HEPES PH 7.0, 200 MM KI.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Details: DUAL SLITS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→34.33 Å / Num. obs: 39193 / % possible obs: 92.8 % / Observed criterion σ(I): 13.4 / Redundancy: 2.2 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.4
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.9 / % possible all: 95

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PV1

3pv1


Resolution: 1.4→27.2 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.624 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22126 1981 5.1 %RANDOM
Rwork0.153 ---
obs0.15652 37168 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.13 Å2
2--0.04 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 5 223 1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021788
X-RAY DIFFRACTIONr_bond_other_d0.0010.021218
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9552427
X-RAY DIFFRACTIONr_angle_other_deg1.21232987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10925.34986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.948158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021958
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02354
X-RAY DIFFRACTIONr_nbd_refined0.3210.2625
X-RAY DIFFRACTIONr_nbd_other0.2360.21151
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2851
X-RAY DIFFRACTIONr_nbtor_other0.110.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4410.291
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5050.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.5091.9221788
X-RAY DIFFRACTIONr_mcbond_other13.8681.9731218
X-RAY DIFFRACTIONr_mcangle_it15.3082.8412420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr16.08333006
X-RAY DIFFRACTIONr_sphericity_free28.951564
X-RAY DIFFRACTIONr_sphericity_bonded13.99953128
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 143 -
Rwork0.205 2714 -
obs--94.42 %

+
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