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- PDB-5cvo: WDR48:USP46~ubiquitin ternary complex -

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Basic information

Entry
Database: PDB / ID: 5cvo
TitleWDR48:USP46~ubiquitin ternary complex
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 46
  • WD repeat-containing protein 48
KeywordsHYDROLASE/PROTEIN BINDING / WDR48 / WD repeat / beta propeller / USP46 / Ubiquitin / covalent complex / DUB / deubiquitinase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / adult feeding behavior / righting reflex / behavioral response to ethanol / deubiquitinase activator activity / hypothalamus gonadotrophin-releasing hormone neuron development / protein deubiquitination / female meiosis I / skeletal system morphogenesis ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / adult feeding behavior / righting reflex / behavioral response to ethanol / deubiquitinase activator activity / hypothalamus gonadotrophin-releasing hormone neuron development / protein deubiquitination / female meiosis I / skeletal system morphogenesis / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / skin development / regulation of synaptic transmission, GABAergic / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / homeostasis of number of cells / positive regulation of double-strand break repair via homologous recombination / single fertilization / behavioral fear response / embryonic organ development / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / neuron projection morphogenesis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / positive regulation of epithelial cell proliferation / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway
Similarity search - Function
WDR48/Bun107 / : / Domain of unknown function (DUF3337) / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain ...WDR48/Bun107 / : / Domain of unknown function (DUF3337) / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 46 / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.885 Å
AuthorsHarris, S.F. / Yin, J.
CitationJournal: Structure / Year: 2015
Title: Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46.
Authors: Yin, J. / Schoeffler, A.J. / Wickliffe, K. / Newton, K. / Starovasnik, M.A. / Dueber, E.C. / Harris, S.F.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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.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: WD repeat-containing protein 48
B: Ubiquitin carboxyl-terminal hydrolase 46
C: Polyubiquitin-B
D: WD repeat-containing protein 48
E: Ubiquitin carboxyl-terminal hydrolase 46
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,3418
Polymers251,2106
Non-polymers1312
Water00
1
A: WD repeat-containing protein 48
B: Ubiquitin carboxyl-terminal hydrolase 46
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,6704
Polymers125,6053
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: WD repeat-containing protein 48
E: Ubiquitin carboxyl-terminal hydrolase 46
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,6704
Polymers125,6053
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.342, 103.764, 190.954
Angle α, β, γ (deg.)90.00, 119.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein WD repeat-containing protein 48 / USP1-associated factor 1 / WD repeat endosomal protein / p80


Mass: 72897.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8TAF3
#2: Protein Ubiquitin carboxyl-terminal hydrolase 46 / Deubiquitinating enzyme 46 / Ubiquitin thioesterase 46 / Ubiquitin-specific-processing protease 46


Mass: 41959.570 Da / Num. of mol.: 2 / Fragment: UNP residues 25-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP46 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62068, ubiquitinyl hydrolase 1
#3: Protein Polyubiquitin-B


Mass: 10748.195 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0CG47
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHESE UNK RESIDUES CORRESPOND TO RESIDUES 563-677 OF UNIPROT ENTRY Q8TAF3. THEY ARE GIVEN UNK ...THESE UNK RESIDUES CORRESPOND TO RESIDUES 563-677 OF UNIPROT ENTRY Q8TAF3. THEY ARE GIVEN UNK IDENTIFIERS BY THE AUTHORS TO SIGNIFY THE UNKNOWN REGISTER OF THIS SECTION OF THE MODEL.

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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: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.88→50 Å / Num. obs: 28480 / % possible obs: 95 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.202 / Net I/σ(I): 8.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CVN

5cvn


Resolution: 3.885→47.704 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 30.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2753 1189 5.19 %
Rwork0.222 --
obs0.2247 22928 68.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.885→47.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15552 0 2 0 15554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515844
X-RAY DIFFRACTIONf_angle_d1.30421457
X-RAY DIFFRACTIONf_dihedral_angle_d17.4545719
X-RAY DIFFRACTIONf_chiral_restr0.0542464
X-RAY DIFFRACTIONf_plane_restr0.0052753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8848-4.06150.2739580.2572981X-RAY DIFFRACTION25
4.0615-4.27550.2871170.22181867X-RAY DIFFRACTION48
4.2755-4.54320.26431420.20162359X-RAY DIFFRACTION60
4.5432-4.89370.26271630.19272726X-RAY DIFFRACTION69
4.8937-5.38550.28371630.20582943X-RAY DIFFRACTION74
5.3855-6.16340.30861630.23663186X-RAY DIFFRACTION80
6.1634-7.75980.29571890.24873737X-RAY DIFFRACTION93
7.7598-47.70710.25611940.22283940X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 186.1363 Å / Origin y: -16.3124 Å / Origin z: 120.5285 Å
111213212223313233
T-0.0372 Å2-0.0485 Å2-0.0284 Å2-0.0298 Å20.0791 Å2---0.0221 Å2
L-0.0186 °2-0.1035 °2-0.0712 °2-0.0925 °20.1794 °2--0.062 °2
S0.0097 Å °0.0494 Å °0.0314 Å °0.1922 Å °0.0939 Å °-0.0706 Å °0.0157 Å °-0.0503 Å °0.1307 Å °
Refinement TLS groupSelection details: all

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