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- PDB-4uf5: Crystal structure of UCH-L5 in complex with inhibitory fragment o... -

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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 / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of DNA replication / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of DNA repair / regulation of proteasomal protein catabolic process / positive regulation of DNA repair / telomere maintenance / Downregulation of TGF-beta receptor signaling / DNA Damage Recognition in GG-NER / UCH proteinases / ubiquitin-dependent protein catabolic process / DNA recombination / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / chromatin remodeling / DNA repair / nucleolus / positive regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase ...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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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