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- PDB-9yc2: Crystal structure of USP49 ZnF-UBP domain -

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Basic information

Entry
Database: PDB / ID: 9yc2
TitleCrystal structure of USP49 ZnF-UBP domain
ComponentsUbiquitin carboxyl-terminal hydrolase 49
KeywordsPROTEIN BINDING / USP49 / deubiquitinase / DUB / protease / ubiquitin / histone / nucleosome / ubiquitin binding domain
Function / homology
Function and homology information


histone H2B deubiquitinase activity / protein deubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA splicing, via spliceosome / histone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis ...histone H2B deubiquitinase activity / protein deubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA splicing, via spliceosome / histone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / nucleoplasm / cytoplasm
Similarity search - Function
: / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / 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 Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 49
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAlexandrovics, J.A. / Komander, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
CitationJournal: To Be Published
Title: The ZnF-UBP domain regulates USP16 activity by dislodging ubiquitin from the active site
Authors: Alexandrovics, J.A. / Agrata, R. / Schenk, P. / Cerra, A. / Nachbur, U. / Babon, J.J. / Komander, D.
History
DepositionSep 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 49
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5487
Polymers12,0681
Non-polymers4806
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.739, 47.220, 55.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 49 / Deubiquitinating enzyme 49 / Ubiquitin thioesterase 49 / Ubiquitin-specific-processing protease 49


Mass: 12068.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GP originates from the 3C cleavage tag / Source: (gene. exp.) Homo sapiens (human) / Gene: USP49 / Plasmid: pOPINK / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q70CQ1, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride; 2 M ammonium sulphate; 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2021 / Details: Micro-collimator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→47.22 Å / Num. obs: 18997 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 13.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.048 / Rrim(I) all: 0.081 / Χ2: 0.99 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4689 / CC1/2: 0.613 / Rpim(I) all: 0.693 / Rrim(I) all: 1.158

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.9 Å / SU ML: 0.1307 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: refined in phenix
RfactorNum. reflection% reflection
Rfree0.1917 967 5.09 %
Rwork0.1532 18030 -
obs0.1551 18997 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.97 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms836 0 19 153 1008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131927
X-RAY DIFFRACTIONf_angle_d1.30791264
X-RAY DIFFRACTIONf_chiral_restr0.0923135
X-RAY DIFFRACTIONf_plane_restr0.0115163
X-RAY DIFFRACTIONf_dihedral_angle_d15.0145360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.470.27461310.23412519X-RAY DIFFRACTION99.66
1.47-1.570.27911320.1982536X-RAY DIFFRACTION99.85
1.57-1.690.20451480.16532538X-RAY DIFFRACTION99.96
1.69-1.860.19921190.14872556X-RAY DIFFRACTION99.93
1.86-2.130.18091380.1372580X-RAY DIFFRACTION100
2.13-2.680.17651570.15322573X-RAY DIFFRACTION99.85
2.68-35.90.18041420.14252728X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.2330376656 Å / Origin y: 24.4516162685 Å / Origin z: 34.9882694025 Å
111213212223313233
T0.130035453313 Å2-0.025356682875 Å2-0.00505246064415 Å2-0.0753325758763 Å20.00801547704703 Å2--0.104397020225 Å2
L1.26172815084 °2-0.949549507416 °20.297847786689 °2-2.64068554708 °2-0.48504630534 °2--2.50135114199 °2
S-0.0155715840739 Å °-0.00382835283104 Å °-0.0501688488045 Å °0.0314804286885 Å °0.0429517256938 Å °0.138995415268 Å °0.0125693823661 Å °-0.0248379457464 Å °-0.0247701951876 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 105)

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