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- PDB-5l8w: Structure of USP12-UB-PRG/UAF1 -

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Basic information

Entry
Database: PDB / ID: 5l8w
TitleStructure of USP12-UB-PRG/UAF1
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 12
  • WD repeat-containing protein 48
KeywordsSTRUCTURAL PROTEIN / DUB-Activator complex USP1 paralog
Function / homology
Function and homology information


regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / seminiferous tubule development / deubiquitinase activator activity / symbiont entry into host cell via disruption of host cell glycocalyx / skeletal system morphogenesis / symbiont entry into host cell via disruption of host cell envelope / skin development / virus tail / homeostasis of number of cells ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / seminiferous tubule development / deubiquitinase activator activity / symbiont entry into host cell via disruption of host cell glycocalyx / skeletal system morphogenesis / symbiont entry into host cell via disruption of host cell envelope / skin development / virus tail / homeostasis of number of cells / protein deubiquitination / embryonic organ development / single fertilization / 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 / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / DNA damage response / proteolysis / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / 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 / 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
Similarity search - Domain/homology
prop-2-en-1-amine / Ubiquitin carboxyl-terminal hydrolase 12 / Tail fiber / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsDharadhar, S. / Sixma, T.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
KWFNKI-2014-6858 Netherlands
KWFNKI 2008-4014 Netherlands
European Research Council249997 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2016
Title: A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme.
Authors: Dharadhar, S. / Clerici, M. / van Dijk, W.J. / Fish, A. / Sixma, T.K.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 2.0Apr 9, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_audit_support / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.entity_id / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_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 12
B: WD repeat-containing protein 48
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6726
Polymers117,4573
Non-polymers2153
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-5 kcal/mol
Surface area40030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.679, 152.820, 182.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Ubiquitin carboxyl-terminal hydrolase 12 / Deubiquitinating enzyme 12 / Ubiquitin thioesterase 12 / Ubiquitin-hydrolyzing enzyme 1 / Ubiquitin- ...Deubiquitinating enzyme 12 / Ubiquitin thioesterase 12 / Ubiquitin-hydrolyzing enzyme 1 / Ubiquitin-specific-processing protease 12


Mass: 43742.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP12, UBH1, USP12L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75317, ubiquitinyl hydrolase 1
#2: Protein WD repeat-containing protein 48 / USP1-associated factor 1 / WD repeat endosomal protein / p80


Mass: 65194.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TAF3
#3: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant expression followed by chemical synthesis
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 4 types, 21 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N
Details: Recombinant expression followed by chemical synthesis
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP. Cryo- 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→47.4 Å / Num. obs: 36148 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.79→2.92 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→47.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 21.115 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R: 0.702 / ESU R Free: 0.34 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25909 1795 5 %RANDOM
Rwork0.20835 ---
obs0.21086 34353 99.18 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.405 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å2-0 Å20 Å2
2--0.65 Å2-0 Å2
3---3.67 Å2
Refinement stepCycle: 1 / Resolution: 2.79→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7258 0 11 18 7287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197411
X-RAY DIFFRACTIONr_bond_other_d0.0020.027115
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.95410023
X-RAY DIFFRACTIONr_angle_other_deg1.009316375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7665900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94924.261345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.033151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7041547
X-RAY DIFFRACTIONr_chiral_restr0.0880.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028293
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021708
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_it3.5896.6953618
X-RAY DIFFRACTIONr_mcbond_other3.5896.6953617
X-RAY DIFFRACTIONr_mcangle_it5.79410.0254512
X-RAY DIFFRACTIONr_mcangle_other5.79310.0244513
X-RAY DIFFRACTIONr_scbond_it3.0746.8963793
X-RAY DIFFRACTIONr_scbond_other3.0746.8963793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.14810.2415512
X-RAY DIFFRACTIONr_long_range_B_refined10.22129812
X-RAY DIFFRACTIONr_long_range_B_other10.22129812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.793→2.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 124 -
Rwork0.329 2308 -
obs--91.46 %
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)
10.76760.0767-0.15390.28340.58511.3671-0.00880.05680.15070.02010.1156-0.01820.08570.2117-0.10680.06770.0228-0.03380.1173-0.04230.0634115.719822.256518.7684
21.5610.5539-0.86140.31470.28833.6355-0.0523-0.0030.11220.0420.01530.04710.3326-0.0650.0370.10210.0217-0.01270.1052-0.04610.0301102.87219.392132.1057
300000000000000-00.0159-0.01360.0350.1914-0.11280.115110.980232.508853.2067
400000000000000-00.0679000.067900.0679000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 370
2X-RAY DIFFRACTION2C14 - 360
3X-RAY DIFFRACTION3D1 - 76
4X-RAY DIFFRACTION4C361 - 559

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