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- PDB-5k1b: Crystal structure of the UAF1/USP12 complex in F222 space group -

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Basic information

Entry
Database: PDB / ID: 5k1b
TitleCrystal structure of the UAF1/USP12 complex in F222 space group
Components
  • Ubiquitin carboxyl-terminal hydrolase 12
  • WD repeat-containing protein 48
KeywordsPROTEIN BINDING/HYDROLASE / WD40 domain / SUMO-like domain / Ubiquitin-Specific Protease 12 / USP12 / USP1-associated factor 1 / Deubiquitinating enzyme / DUB / PROTEIN BINDING-HYDROLASE complex
Function / homology
Function and homology information


Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / positive regulation of receptor signaling pathway via JAK-STAT / ubiquitin binding / regulation of protein stability / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination ...Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / positive regulation of receptor signaling pathway via JAK-STAT / ubiquitin binding / regulation of protein stability / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / positive regulation of canonical Wnt signaling pathway / late endosome / single-stranded DNA binding / double-stranded DNA binding / ubiquitinyl hydrolase 1 / lysosome / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / DNA damage response / proteolysis / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
WDR48/Bun107 / : / WDR48/Bun107, ubiquitin-like domain / : / 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 / : / WDR48/Bun107, ubiquitin-like domain / : / 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. / Papain-like cysteine peptidase superfamily / 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
Ubiquitin carboxyl-terminal hydrolase 12 / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsLi, H. / D'Andrea, A.D. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2016
Title: Allosteric Activation of Ubiquitin-Specific Proteases by beta-Propeller Proteins UAF1 and WDR20.
Authors: Li, H. / Lim, K.S. / Kim, H. / Hinds, T.R. / Jo, U. / Mao, H. / Weller, C.E. / Sun, J. / Chatterjee, C. / D'Andrea, A.D. / Zheng, N.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: WD repeat-containing protein 48
A: Ubiquitin carboxyl-terminal hydrolase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9183
Polymers118,8532
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.958, 158.929, 234.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 76312.398 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: Escherichia coli K-12 (bacteria) / References: UniProt: Q8TAF3
#2: 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: 42540.254 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: Escherichia coli K-12 (bacteria) / References: UniProt: O75317, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M imidazole, 18% PEG 2000MME, 0.3 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 3.3→50.01 Å / Num. obs: 16052 / % possible obs: 98.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.102 / Rsym value: 0.109 / Net I/σ(I): 28.2
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 6.1 % / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Cootmodel building
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→50.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28551 814 4.8 %RANDOM
Rwork0.23498 ---
obs0.23737 16052 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 128.676 Å2
Baniso -1Baniso -2Baniso -3
1--7.03 Å20 Å20 Å2
2--2.08 Å20 Å2
3---4.95 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6365 0 1 0 6366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196486
X-RAY DIFFRACTIONr_bond_other_d00.025972
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9488829
X-RAY DIFFRACTIONr_angle_other_deg3.903313643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5245824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0224.487263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.379151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3881527
X-RAY DIFFRACTIONr_chiral_restr0.1040.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027321
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021450
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_it7.89613.4283353
X-RAY DIFFRACTIONr_mcbond_other7.89613.4263352
X-RAY DIFFRACTIONr_mcangle_it11.73320.1274158
X-RAY DIFFRACTIONr_mcangle_other11.73220.1294159
X-RAY DIFFRACTIONr_scbond_it7.82813.5983133
X-RAY DIFFRACTIONr_scbond_other7.82913.5933131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.73720.2624670
X-RAY DIFFRACTIONr_long_range_B_refined14.7267042
X-RAY DIFFRACTIONr_long_range_B_other14.7277042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 57 -
Rwork0.314 1149 -
obs--96.4 %

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