[English] 日本語
Yorodumi
- PDB-4uf5: Crystal structure of UCH-L5 in complex with inhibitory fragment o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uf5
TitleCrystal structure of UCH-L5 in complex with inhibitory fragment of INO80G
Components
  • NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
KeywordsHYDROLASE / DEUBIQUITINATING ENZYME
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / positive regulation of smoothened signaling pathway / endopeptidase inhibitor activity / proteasome binding / regulation of chromosome organization / midbrain development ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / positive regulation of smoothened signaling pathway / endopeptidase inhibitor activity / proteasome binding / regulation of chromosome organization / midbrain development / regulation of DNA replication / regulation of embryonic development / protein deubiquitination / regulation of DNA repair / regulation of proteasomal protein catabolic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance / proteasome complex / positive regulation of DNA repair / Downregulation of TGF-beta receptor signaling / DNA Damage Recognition in GG-NER / UCH proteinases / protease binding / ubiquitin-dependent protein catabolic process / DNA recombination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / chromatin remodeling / DNA repair / positive regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear factor related to kappa-B-binding protein / NFRKB winged helix-like domain / NFRKB winged helix-like domain superfamily / NFRKB Winged Helix-like / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 ...Nuclear factor related to kappa-B-binding protein / NFRKB winged helix-like domain / NFRKB winged helix-like domain superfamily / NFRKB Winged Helix-like / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear factor related to kappa-B-binding protein / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsSahtoe, D.D. / Van Dijk, W.J. / El Oualid, F. / Ekkebus, R. / Ovaa, H. / Sixma, T.K.
CitationJournal: Mol.Cell / Year: 2015
Title: Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G.
Authors: Sahtoe, D.D. / Van Dijk, W.J. / El Oualid, F. / Ekkebus, R. / Ovaa, H. / Sixma, T.K.
History
DepositionDec 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
B: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,4992
Polymers53,4992
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-34.4 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.302, 95.302, 132.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 / UCH-L5 / UBIQUITIN C-TERMINAL HYDROLASE UCH37 / UBIQUITIN THIOESTERASE L5 / UCH-L5


Mass: 37734.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ISOFORM 3 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-NKI-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Protein NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN / DNA-BINDING PROTEIN R KAPPA-B / INO80 COMPLEX SUBUNIT G / INO 80G


Mass: 15763.703 Da / Num. of mol.: 1 / Fragment: DEUBAD DOMAIN, RESIDUES 40-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-NKI-HIS-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q6P4R8
Sequence detailsISOFORM 3 OF UCH-L5 HAS BEEN CRYSTALLIZED

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growTemperature: 277 K
Details: 100 MM TRIS PH 9.0, 200 MM LITHIUM CHLORIDE, 17% PEG 8000. 4 DEGREES CELSIUS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.91165
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 3.7→47.65 Å / Num. obs: 7004 / % possible obs: 100 % / Observed criterion σ(I): 2.4 / Redundancy: 6.7 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 7.4
Reflection shellResolution: 3.7→4.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IHR

3ihr


Resolution: 3.7→95.3 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.786 / SU B: 157.884 / SU ML: 0.978 / Cross valid method: THROUGHOUT / ESU R Free: 0.998 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.35691 737 10.6 %RANDOM
Rwork0.30656 ---
obs0.31184 6223 99.87 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 3.7→95.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 0 0 3296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193364
X-RAY DIFFRACTIONr_bond_other_d0.0010.023220
X-RAY DIFFRACTIONr_angle_refined_deg0.7281.9494531
X-RAY DIFFRACTIONr_angle_other_deg0.65437403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2735399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39224.917181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4715617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0361520
X-RAY DIFFRACTIONr_chiral_restr0.0420.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 46 -
Rwork0.385 456 -
obs--99.6 %
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)
11.9171-0.1394-0.42531.70320.21861.5470.13090.0920.12680.1611-0.0489-0.211-0.15290.2584-0.08190.07350.03640.04570.18230.10890.1228-21.84333.626-5.345
22.4055-2.7003-0.6516.7964-0.97431.643-0.19530.236-0.49550.0397-0.1753-0.09450.5586-0.07830.37060.3177-0.0831-0.00660.19480.02810.2723-28.09916.152.733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 320
2X-RAY DIFFRACTION2B44 - 153

+
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