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- PDB-5cvn: WDR48 (2-580):USP46~ubiquitin ternary complex -

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Basic information

Entry
Database: PDB / ID: 5cvn
TitleWDR48 (2-580):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 / seminiferous tubule development / deubiquitinase activator activity / symbiont entry into host cell via disruption of host cell glycocalyx / skeletal system morphogenesis / skin development ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / adult feeding behavior / righting reflex / behavioral response to ethanol / seminiferous tubule development / deubiquitinase activator activity / symbiont entry into host cell via disruption of host cell glycocalyx / skeletal system morphogenesis / skin development / regulation of synaptic transmission, GABAergic / symbiont entry into host cell via disruption of host cell envelope / virus tail / regulation of postsynaptic neurotransmitter receptor internalization / homeostasis of number of cells / protein deubiquitination / embryonic organ development / single fertilization / behavioral fear response / positive regulation of double-strand break repair via homologous recombination / Fanconi Anemia Pathway / ubiquitin binding / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of epithelial cell proliferation / double-strand break repair via homologous recombination / positive regulation of receptor signaling pathway via JAK-STAT / regulation of protein stability / multicellular organism growth / late endosome / single-stranded DNA binding / double-stranded DNA binding / spermatogenesis / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / intracellular membrane-bounded organelle / DNA damage response / glutamatergic synapse / proteolysis / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
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. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Cysteine proteinases / Cathepsin B; Chain A / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily / Ubiquitin family / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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
Tail fiber / Ubiquitin carboxyl-terminal hydrolase 46 / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 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
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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9244
Polymers119,8593
Non-polymers651
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.437, 154.189, 182.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1012-

HOH

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Components

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


Mass: 67150.906 Da / Num. of mol.: 1 / Fragment: UNP residues 2-580
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.: 1 / 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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→47.36 Å / Num. obs: 21052 / Biso Wilson estimate: 87.8 Å2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.35-3.477.70.71920641.08299.9
3.47-3.617.90.48820941.148100
3.61-3.777.90.36820541.214100
3.77-3.977.90.27620791.201100
3.97-4.227.90.20120941.236100
4.22-4.557.80.1320901.38100
4.55-57.80.10521151.344100
5-5.737.70.10921111.358100
5.73-7.217.60.09521361.31100
7.21-507.30.04522281.048100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5CVL, 1NBF

5cvl

1nbf


Resolution: 3.36→47.36 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1060 5.04 %RANDOM
Rwork0.1749 ---
obs0.1772 21052 99.19 %-
Displacement parametersBiso mean: 103.39 Å2
Baniso -1Baniso -2Baniso -3
1-17.7952 Å20 Å20 Å2
2---0.2457 Å20 Å2
3----17.5495 Å2
Refine analyzeLuzzati coordinate error obs: 0.707 Å
Refinement stepCycle: LAST / Resolution: 3.36→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 1 34 7323
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097432HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1710054HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2642SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes199HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1053HARMONIC5
X-RAY DIFFRACTIONt_it7432HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion22.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion978SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8357SEMIHARMONIC4
LS refinement shellResolution: 3.36→3.52 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2598 132 5.03 %
Rwork0.208 2491 -
all0.2107 2623 -
obs--99.19 %
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)
13.63220.2111-0.93232.5797-0.78171.9090.17760.81350.4668-0.2210.11760.0225-0.0263-0.6009-0.2953-0.36580.0089-0.0111-0.05410.3038-0.2507105.808191.86929.4597
22.1411-0.1114-0.3011.8879-1.03094.33180.001-0.11940.24070.18480.29530.10050.1317-0.544-0.2963-0.2216-0.0319-0.107-0.10850.0325-0.137391.1598176.7172.6142
33.73-1.5661-0.46492.827-2.64047.0079-0.01710.01160.0202-0.19740.0161-0.31640.31050.06190.0009-0.0433-0.0138-0.0555-0.05240.05150.0251103.537175.22758.4376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }

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