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- PDB-4uf6: UCH-L5 in complex with ubiquitin-propargyl bound to an activating... -

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Basic information

Entry
Database: PDB / ID: 4uf6
TitleUCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G
Components
  • NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN
  • POLYUBIQUITIN-B
  • 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 / symbiont entry into host cell via disruption of host cell glycocalyx / endopeptidase inhibitor activity / symbiont entry into host cell via disruption of host cell envelope / virus tail ...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 / symbiont entry into host cell via disruption of host cell glycocalyx / endopeptidase inhibitor activity / symbiont entry into host cell via disruption of host cell envelope / virus tail / proteasome binding / regulation of chromosome organization / midbrain development / regulation of DNA replication / regulation of embryonic development / protein deubiquitination / regulation of proteasomal protein catabolic process / regulation of DNA repair / Downregulation of TGF-beta receptor signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance / proteasome complex / positive regulation of DNA repair / 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 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases ...Nuclear factor related to kappa-B-binding protein / NFRKB winged helix-like domain / NFRKB winged helix-like domain superfamily / NFRKB Winged Helix-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin family / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tail fiber / 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: 3.69 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 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 1, 2024Group: 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_conn
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_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
Revision 1.5Oct 23, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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: POLYUBIQUITIN-B
C: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN
D: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
E: POLYUBIQUITIN-B
F: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN
G: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
H: POLYUBIQUITIN-B
I: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN
J: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
K: POLYUBIQUITIN-B
L: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)215,07112
Polymers215,07112
Non-polymers00
Water00
1
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
B: POLYUBIQUITIN-B
C: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,7683
Polymers53,7683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
E: POLYUBIQUITIN-B
F: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,7683
Polymers53,7683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
G: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
H: POLYUBIQUITIN-B
I: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,7683
Polymers53,7683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
J: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
K: POLYUBIQUITIN-B
L: NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,7683
Polymers53,7683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)152.084, 137.788, 98.916
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number5
Space group name H-MC121

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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.: 4
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE CYS88 COVALENTLY LINKED TO UBIQUITIN-PROPARGYL
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
POLYUBIQUITIN-B / UBIQUITIN


Mass: 8558.857 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: GLY76 OF UBIQUITIN IS REPLACED BY GLY-AYE THAT IS COVALENTLY LINKED TO THE ACTIVE SITE CYS88 OF UCH- L5
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0CG47
#3: Protein
NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN / DNA-BINDING PROTEIN R KAPPA-B / INO80 COMPLEX SUBUNIT G / INO80G


Mass: 7474.066 Da / Num. of mol.: 4
Fragment: ACTIVATING FRAGMENT OF INO80G DEUBAD DOMAIN, RESIDUES 40-101
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
Has protein modificationY
Nonpolymer detailsPROP-2-EN-1-AMINE (AYE): AYE REPLACE UBIQUITIN GLY76
Sequence detailsISOFORM 3 GLY76 IN NATIVE UBIQUITIN IS REPLACED BY AYE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 277 K
Details: 100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.69→47.74 Å / Num. obs: 21090 / % possible obs: 97 % / Observed criterion σ(I): 1.8 / Redundancy: 4.2 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.8
Reflection shellResolution: 3.69→3.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.8 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF THE UCH-L5-UBIQUITIN FROM THE

Resolution: 3.69→100.99 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.876 / SU B: 118.096 / SU ML: 0.739 / Cross valid method: THROUGHOUT / ESU R Free: 0.835 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4-FOLD NCS WAS PRESENT IN THE ASYMMETRIC UNIT. LOCAL NCS RESTRAINTS WERE APPLIED IN REFMAC DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.26907 1059 5 %RANDOM
Rwork0.238 ---
obs0.23956 20030 97.9 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.548 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å22.63 Å2
2---1.53 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 3.69→100.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13486 0 0 0 13486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913739
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213311
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.96318520
X-RAY DIFFRACTIONr_angle_other_deg0.891330666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62651648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24625.355704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9152569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0821576
X-RAY DIFFRACTIONr_chiral_restr0.0620.22050
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215497
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023131
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: 3.689→3.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 46 -
Rwork0.332 1125 -
obs--73.56 %
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)
14.5995-0.631-2.19023.62631.14324.04480.20560.77550.6299-0.29470.03390.0802-0.1519-0.429-0.23950.0871-0.00760.01420.93320.23230.1126108.358101.168-0.082
25.31980.7581-0.212310.75154.93912.43740.30560.39461.6742-2.0382-0.26010.2813-1.3809-0.3104-0.04541.89510.4847-0.01381.09450.61290.95107.843122.526-4.95
38.7034-1.9487-2.21552.85581.48845.08580.59560.68540.38770.0583-0.0048-0.3099-0.73970.4278-0.59071.01290.0140.02421.01860.14590.8044102.141121.3221.123
43.44791.2508-1.16113.6913-1.06763.0340.1919-0.14450.25310.0284-0.026-0.0606-0.1083-0.3208-0.16580.1540.0792-0.00540.5872-0.09070.0484108.48298.52553.726
53.6758-0.1487-1.57728.14040.49171.3010.1343-0.2040.7109-0.01340.0091-0.7384-0.7456-0.0184-0.14340.81260.0438-0.13510.5917-0.13410.5242115.734117.36763.119
610.6512.1127-6.33142.2210.25525.14090.0376-0.31311.4376-0.10590.44490.6314-0.20360.3685-0.48251.09-0.02090.11350.86790.0990.8035122.228118.40635.231
76.18220.2541-3.65210.0699-0.066611.8755-0.080.3866-0.92510.16030.13520.10811.517-0.2925-0.05521.008-0.06260.24570.9459-0.18961.274293.94569.41715.366
84.4050.1458-1.23774.26921.89274.6644-0.1472-0.20990.3517-0.1692-0.02810.07250.2195-0.34410.17540.0543-0.06250.01490.72560.06910.080881.51491.72632.768
90.40591.1569-0.50129.2311-2.32711.6822-0.18170.1072-0.3853-0.22260.13730.10870.61970.1520.04440.5956-0.21630.01470.827-0.12120.712769.12773.6827.913
104.9146-2.64581.47597.38554.25299.10010.3120.8454-1.0752-0.64860.0681-0.12161.16640.7088-0.38020.7392-0.03220.13420.9222-0.04361.1105116.04265.92135.548
112.82580.3097-0.63024.4410.29823.1877-0.01910.18850.0266-0.01250.1125-0.18330.39740.2427-0.09350.05380.0028-0.00590.5191-0.0580.0149132.7485.69519.348
122.084-0.6860.60297.8096-0.68882.50610.1192-0.152-0.79750.38310.06140.04370.87210.0265-0.18050.45890.071-0.19450.58420.00280.5311139.91264.90721.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 319
2X-RAY DIFFRACTION2B1 - 75
3X-RAY DIFFRACTION3C44 - 93
4X-RAY DIFFRACTION4D6 - 321
5X-RAY DIFFRACTION5E1 - 75
6X-RAY DIFFRACTION6F44 - 93
7X-RAY DIFFRACTION7I45 - 93
8X-RAY DIFFRACTION8G6 - 318
9X-RAY DIFFRACTION9H1 - 75
10X-RAY DIFFRACTION10L45 - 93
11X-RAY DIFFRACTION11J6 - 319
12X-RAY DIFFRACTION12K1 - 75

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