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- PDB-5k1a: Crystal structure of the UAF1-USP12 complex in C2 space group -

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Basic information

Entry
Database: PDB / ID: 5k1a
TitleCrystal structure of the UAF1-USP12 complex in C2 space group
Components
  • Ubiquitin carboxyl-terminal hydrolase 12
  • WD repeat-containing protein 48
KeywordsHYDROLASE / WD40 domain / Ubiquitin-specific protease 12 / USP12 / USP1-associated factor 1 / USP1 / Deubiquitinating enzyme / DUB / SUMO-like domain / SLD
Function / homology
Function and homology information


regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization / embryonic organ development / ubiquitin binding / positive regulation of epithelial cell proliferation / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of receptor signaling pathway via JAK-STAT / double-strand break repair via homologous recombination / multicellular organism growth / late endosome / single-stranded DNA binding / spermatogenesis / double-stranded DNA binding / 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 / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
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 / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily ...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. / Papain-like cysteine peptidase superfamily / 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. / WD domain, G-beta repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.4Sep 27, 2023Group: 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 12
B: WD repeat-containing protein 48
C: Ubiquitin carboxyl-terminal hydrolase 12
D: WD repeat-containing protein 48
E: Ubiquitin carboxyl-terminal hydrolase 12
F: WD repeat-containing protein 48
G: Ubiquitin carboxyl-terminal hydrolase 12
H: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,88612
Polymers459,6258
Non-polymers2624
Water28,4821581
1
A: Ubiquitin carboxyl-terminal hydrolase 12
B: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9723
Polymers114,9062
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin carboxyl-terminal hydrolase 12
D: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9723
Polymers114,9062
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ubiquitin carboxyl-terminal hydrolase 12
F: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9723
Polymers114,9062
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ubiquitin carboxyl-terminal hydrolase 12
H: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9723
Polymers114,9062
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)262.425, 103.301, 178.466
Angle α, β, γ (deg.)90.00, 117.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: 38593.773 Da / Num. of mol.: 4 / Fragment: residues 40-370
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
#2: Protein
WD repeat-containing protein 48 / USP1-associated factor 1 / WD repeat endosomal protein / p80


Mass: 76312.398 Da / Num. of mol.: 4
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1581 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium citrate, 7% PEG 3350, 0.15 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 187452 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.106 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.7 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
Cootmodel building
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K16 and 5K1B

5k16

5k1b


Resolution: 2.3→49.104 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 9401 5.02 %
Rwork0.1875 --
obs0.1901 187452 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26060 0 4 1581 27645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926622
X-RAY DIFFRACTIONf_angle_d1.15836044
X-RAY DIFFRACTIONf_dihedral_angle_d14.3749644
X-RAY DIFFRACTIONf_chiral_restr0.0464150
X-RAY DIFFRACTIONf_plane_restr0.0054526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.3272930.24325829X-RAY DIFFRACTION99
2.3261-2.35350.33312940.2515951X-RAY DIFFRACTION99
2.3535-2.38220.29462990.24325843X-RAY DIFFRACTION99
2.3822-2.41240.28873190.23275900X-RAY DIFFRACTION100
2.4124-2.44410.30872940.23635939X-RAY DIFFRACTION100
2.4441-2.47760.28443020.23035951X-RAY DIFFRACTION100
2.4776-2.5130.31053360.2275910X-RAY DIFFRACTION100
2.513-2.55050.27043150.21515877X-RAY DIFFRACTION100
2.5505-2.59030.27773200.21895886X-RAY DIFFRACTION100
2.5903-2.63280.30052950.22185978X-RAY DIFFRACTION100
2.6328-2.67820.29783240.23035853X-RAY DIFFRACTION100
2.6782-2.72690.26053440.22945917X-RAY DIFFRACTION100
2.7269-2.77930.27273360.22135894X-RAY DIFFRACTION100
2.7793-2.83610.27832980.23035938X-RAY DIFFRACTION100
2.8361-2.89770.27963250.21545944X-RAY DIFFRACTION100
2.8977-2.96510.28182960.20925911X-RAY DIFFRACTION100
2.9651-3.03930.28123220.21825974X-RAY DIFFRACTION100
3.0393-3.12140.28523130.21245916X-RAY DIFFRACTION100
3.1214-3.21330.26283130.2125954X-RAY DIFFRACTION100
3.2133-3.31690.26393350.19295883X-RAY DIFFRACTION100
3.3169-3.43550.2553190.19325990X-RAY DIFFRACTION100
3.4355-3.5730.23913290.18055888X-RAY DIFFRACTION100
3.573-3.73550.23083080.17255919X-RAY DIFFRACTION100
3.7355-3.93240.2053210.1675951X-RAY DIFFRACTION100
3.9324-4.17870.20533040.15965937X-RAY DIFFRACTION100
4.1787-4.50110.18363150.145979X-RAY DIFFRACTION100
4.5011-4.95370.1843000.13526002X-RAY DIFFRACTION100
4.9537-5.66960.19643190.15975980X-RAY DIFFRACTION100
5.6696-7.13960.22063100.1746026X-RAY DIFFRACTION100
7.1396-49.11550.20283030.18246131X-RAY DIFFRACTION99

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