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- PDB-6qml: UCHL3 in complex with synthetic, K27-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 6qml
TitleUCHL3 in complex with synthetic, K27-linked diubiquitin
Components
  • (Polyubiquitin- ...) x 2
  • Ubiquitin carboxyl-terminal hydrolase isozyme L3
KeywordsHYDROLASE / Deubiquitinase Inhibition / PROTEIN BINDING
Function / homology
Function and homology information


deNEDDylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / protein deubiquitination / male meiosis I ...deNEDDylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / post-translational protein modification / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / : / Polyubiquitin-B / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase isozyme L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMurachelli, A.G. / Sixma, T.K.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Oncode Institute Netherlands
CancerGenomiCs.nl Netherlands
CitationJournal: Cell Chem Biol / Year: 2021
Title: K27-Linked Diubiquitin Inhibits UCHL3 via an Unusual Kinetic Trap.
Authors: van Tilburg, G.B.A. / Murachelli, A.G. / Fish, A. / van der Heden van Noort, G.J. / Ovaa, H. / Sixma, T.K.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.2Mar 10, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 L3
B: Polyubiquitin-B
C: Polyubiquitin-C
D: Ubiquitin carboxyl-terminal hydrolase isozyme L3
E: Polyubiquitin-B
F: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,58132
Polymers86,0646
Non-polymers1,51726
Water4,234235
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L3
B: Polyubiquitin-B
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,94418
Polymers43,0323
Non-polymers91215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ubiquitin carboxyl-terminal hydrolase isozyme L3
E: Polyubiquitin-B
F: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,63714
Polymers43,0323
Non-polymers60511
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.290, 81.206, 159.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23E
14C
24F
15D
25E
16D
26F
17E
27F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 230
2010B4 - 230
1020C1 - 76
2020D1 - 76
1030C1 - 76
2030E1 - 76
1040C1 - 76
2040F1 - 76
1050D1 - 76
2050E1 - 76
1060D1 - 76
2060F1 - 76
1070E1 - 76
2070F1 - 76

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L3 / UCH-L3 / Ubiquitin thioesterase L3


Mass: 25896.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL3 / Plasmid: pGEX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15374, ubiquitinyl hydrolase 1

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Polyubiquitin- ... , 2 types, 4 molecules BECF

#2: Protein Polyubiquitin-B


Mass: 8558.793 Da / Num. of mol.: 2 / Mutation: M1(NLE) / Source method: obtained synthetically / Details: Met 1 substituted with Norleucine (NLE) / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47
#3: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48

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Non-polymers , 5 types, 261 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Mutation: M1(NLE) / Source method: obtained synthetically / Formula: K / Details: Met 1 substituted with Norleucine (NLE) / Source: (synth.) Homo sapiens (human)
#5: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.04 %
Description: Needles and plates growing together. Relative ratio can be changed by small difference in PEG concentration. Multiple lattices common.
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and ...Details: Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 22, 2017
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→79.929 Å / Num. obs: 54231 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.115 / Rsym value: 0.092 / Net I/av σ(I): 6 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 0.7 / Num. measured all: 11726 / Num. unique obs: 1893 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Rsym value: 0.99 / Net I/σ(I) obs: 28 / % possible all: 100

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 1UCH

1ubq

1uch


Resolution: 2.1→44.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.828 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.176
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2684 5 %RANDOM
Rwork0.1843 ---
obs0.1866 51455 99.79 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 139.96 Å2 / Biso mean: 55.422 Å2 / Biso min: 25.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.1→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 71 235 6350
Biso mean--66.58 51.38 -
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136257
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175931
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6568440
X-RAY DIFFRACTIONr_angle_other_deg1.2311.57813840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91823.473334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.317151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8331536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73090.06
12B73090.06
21C21300.11
22D21300.11
31C21520.1
32E21520.1
41C21520.11
42F21520.11
51D20900.12
52E20900.12
61D22060.07
62F22060.07
71E21080.12
72F21080.12
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 208 -
Rwork0.299 3764 -
all-3972 -
obs--100 %
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)
11.48720.54480.30281.8802-0.41271.61020.0524-0.06340.04220.1556-0.0395-0.02360.05090.0238-0.01290.1640.01550.00910.12370.00490.0043-3.962-16.3710.631
22.6187-0.81380.02921.92590.54691.29490.210.50870.1912-0.1832-0.0385-0.084-0.02380.0411-0.17150.18020.0530.02680.27630.05150.040927.803-13.794-13.89
33.3804-0.60861.25173.0295-2.65365.65080.0223-0.406-0.35340.5631-0.0059-0.18790.2235-0.0798-0.01640.4653-0.0227-0.08980.27050.0420.0633-4.377-30.62434.138
45.54080.7552.92972.0378-0.14556.93780.4897-0.4037-0.55460.1495-0.00630.31530.7969-0.557-0.48340.397-0.0588-0.07050.19710.05490.1578-32.052-31.33514.546
55.39891.17620.70293.15182.42375.61890.16931.4987-0.2965-0.67160.0891-0.06330.1033-0.1784-0.25840.50290.1469-0.0651.0813-0.02320.045527.887-23.107-39.509
65.547-0.5757-0.01843.0570.33817.4570.13660.4601-0.1926-0.1657-0.08880.00710.38270.1425-0.04780.30720.03430.04230.1977-0.04360.046955.933-27.313-21.081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 230
2X-RAY DIFFRACTION2B4 - 230
3X-RAY DIFFRACTION3C1 - 76
4X-RAY DIFFRACTION4D1 - 76
5X-RAY DIFFRACTION5E1 - 76
6X-RAY DIFFRACTION6F1 - 76

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