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- PDB-4uel: UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEU... -

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Basic information

Entry
Database: PDB / ID: 4uel
TitleUCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
Components
  • POLYUBIQUITIN-B
  • PROTEASOMAL UBIQUITIN RECEPTOR ADRM1
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
KeywordsHYDROLASE / DEUBIQUITINATING ENZYME / DUB / UCH37 / UCHL5 / PROTEASOME / ADRM1 / RPN13 / DEUBAD / UCH / UBIQUITIN-PROPARGYL
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 / proteasome regulatory particle, lid subcomplex / symbiont entry into host cell via disruption of host cell glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly ...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 / proteasome regulatory particle, lid subcomplex / symbiont entry into host cell via disruption of host cell glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / endopeptidase inhibitor activity / molecular function 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 / endopeptidase activator activity / proteasome assembly / regulation of DNA repair / Downregulation of TGF-beta receptor signaling / Regulation of activated PAK-2p34 by proteasome mediated degradation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / telomere maintenance / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / proteasome complex / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / TNFR2 non-canonical NF-kB pathway / positive regulation of DNA repair / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / transcription elongation by RNA polymerase II / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / protease binding / ubiquitin-dependent protein catabolic process / DNA recombination / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / regulation of cell cycle / chromatin remodeling / DNA repair / positive regulation of DNA-templated transcription / nucleolus / RNA binding
Similarity search - Function
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 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 ...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 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / 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 / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / 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 / Proteasomal ubiquitin receptor ADRM1 / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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

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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: PROTEASOMAL UBIQUITIN RECEPTOR ADRM1


Theoretical massNumber of molelcules
Total (without water)59,3593
Polymers59,3593
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-50.2 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.340, 98.600, 100.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37734.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE CYS88 COVALENTLY LINKED TO UBIQUITIN-PROPARGYL
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: ISOFORM 3 / 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.: 1 / Mutation: YES / 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 PROTEASOMAL UBIQUITIN RECEPTOR ADRM1 / RPN13 / 110 KDA CELL MEMBRANE GLYCOPROTEIN / GP110 / ADHESION-REGULATING MOLECULE 1 / ARM-1 / ...RPN13 / 110 KDA CELL MEMBRANE GLYCOPROTEIN / GP110 / ADHESION-REGULATING MOLECULE 1 / ARM-1 / PROTEASOME REGULATORY PARTICLE NON-ATPASE 13 / HRPN13 / RPN13 HOMOLOG


Mass: 13065.674 Da / Num. of mol.: 1 / Fragment: DEUBAD DOMAIN, RESIDUES 266-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF-NKI-HIS-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q16186
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGLY76 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: 49 %
Description: MOLECULAR REPLACEMENT WAS PERFORMED WITH THE PARTIALLY BUILD UCH-L5-RPN13 STRUCTURE, SEE RELATED PDB
Crystal growTemperature: 277 K
Details: 100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0
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 Å / Relative weight: 1
ReflectionResolution: 2.3→45.34 Å / Num. obs: 26979 / % possible obs: 99.8 % / Observed criterion σ(I): 1.6 / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→70.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.37 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 1354 5 %RANDOM
Rwork0.19141 ---
obs0.19365 25531 99.74 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.613 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2---0.63 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→70.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 234 3996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193830
X-RAY DIFFRACTIONr_bond_other_d0.0010.023717
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.975169
X-RAY DIFFRACTIONr_angle_other_deg0.68338570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0845472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0625.668187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.081519
X-RAY DIFFRACTIONr_chiral_restr0.0550.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
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_it2.9321.8771897
X-RAY DIFFRACTIONr_mcbond_other2.9331.8771896
X-RAY DIFFRACTIONr_mcangle_it4.2782.7992363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0212.2731933
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: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 97 -
Rwork0.286 1827 -
obs--98.36 %
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)
11.323-0.3286-0.54951.45340.34451.4525-0.0639-0.05640.0045-0.02980.0338-0.03960.11740.07020.03010.13060.0252-0.00070.0793-0.01820.0229-0.1797.48630.211
23.716-3.65271.99196.4542-2.56441.2248-0.00450.1630.09470.0251-0.1083-0.2318-0.07760.08110.11270.37320.0026-0.01760.2614-0.02410.06644.17589.9766.673
35.014-3.64473.21682.7039-2.37032.14720.26350.5891-0.3876-0.0772-0.27840.23480.06730.39890.01490.9239-0.07410.17730.7959-0.00191.144136.31178.63514.855
42.21420.1824-1.23452.5717-0.8973.6940.03180.01810.1706-0.26480.0368-0.2127-0.0290.3038-0.06850.1585-0.00720.03160.1096-0.0140.102319.81897.34611.973
510.31751.73290.85090.4522-0.73695.265-0.0507-0.04570.99370.0265-0.2630.0574-0.27331.38120.31370.6208-0.05740.06060.5308-0.00130.761923.50273.5727.055
61.6690.15240.74215.685-0.87172.44230.12040.0208-0.0228-0.1824-0.1262-0.361-0.05520.03190.00580.0714-0.01560.03190.0936-0.0070.087115.09871.73214.748
79.9702-0.5523-6.80670.26680.799316.5324-0.4380.12720.28990.2606-0.0954-0.47080.37040.4360.53350.4375-0.0037-0.44560.37640.22611.162329.90862.18720.665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 228
2X-RAY DIFFRACTION2A229 - 315
3X-RAY DIFFRACTION3A316 - 320
4X-RAY DIFFRACTION4B1 - 75
5X-RAY DIFFRACTION5C287 - 307
6X-RAY DIFFRACTION6C308 - 363
7X-RAY DIFFRACTION7C364 - 384

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