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- PDB-2qiy: yeast Deubiquitinase Ubp3 and Bre5 cofactor complex -

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Basic information

Entry
Database: PDB / ID: 2qiy
Titleyeast Deubiquitinase Ubp3 and Bre5 cofactor complex
Components
  • UBP3-associated protein BRE5
  • Ubiquitin carboxyl-terminal hydrolase 3
KeywordsSignaling protein/hydrolase / deubiquitylation / ubiquitin-specific processing proteases(UBPs) / NTF2 / protein-protein recognition / Hydrolase / Thiol protease / Ubl conjugation pathway / Phosphorylation / RNA-binding / Signaling protein-hydrolase COMPLEX
Function / homology
Function and homology information


Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / regulation of response to osmotic stress / ribophagy / protein retention in Golgi apparatus / regulation of ER to Golgi vesicle-mediated transport / Termination of translesion DNA synthesis / negative regulation of mitophagy / protein deubiquitination / Ub-specific processing proteases ...Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / regulation of response to osmotic stress / ribophagy / protein retention in Golgi apparatus / regulation of ER to Golgi vesicle-mediated transport / Termination of translesion DNA synthesis / negative regulation of mitophagy / protein deubiquitination / Ub-specific processing proteases / stress granule assembly / P-body / regulation of protein stability / cytoplasmic stress granule / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA binding / mitochondrion / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 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 ...Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 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. / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Roll / Alpha Beta
Similarity search - Domain/homology
UBP3-associated protein BRE5 / Ubiquitin carboxyl-terminal hydrolase 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLi, K. / Liu, X. / Marmorstein, R.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme.
Authors: Li, K. / Ossareh-Nazari, B. / Liu, X. / Dargemont, C. / Marmorstein, R.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Structural basis for interaction between the Ubp3 deubiqutinating enzyme and its Bre5 cofactor
Authors: Li, K. / Zhao, K. / Ossareh-Nazari, B. / Da, G. / Dargemont, C. / Marmorstein, R.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBP3-associated protein BRE5
C: Ubiquitin carboxyl-terminal hydrolase 3
B: UBP3-associated protein BRE5
D: Ubiquitin carboxyl-terminal hydrolase 3


Theoretical massNumber of molelcules
Total (without water)45,8984
Polymers45,8984
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 90.240, 101.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBP3-associated protein BRE5 / Brefeldin-A sensitivity protein 5


Mass: 17675.080 Da / Num. of mol.: 2 / Fragment: residues 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRE5 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53741
#2: Protein/peptide Ubiquitin carboxyl-terminal hydrolase 3 / Ubiquitin thioesterase 3 / Ubiquitin-specific-processing protease 3 / Deubiquitinating enzyme 3


Mass: 5273.989 Da / Num. of mol.: 2 / Fragment: residues 190-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBP3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01477, EC: 3.1.2.15
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 9
Details: 10%(w/v) PEG 20000, 100mM Bicine, 2% Dioxan, pH 9.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 1.69→49.45 Å / Num. all: 59376 / Num. obs: 50599 / Redundancy: 3.9 %
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1ZX2

1zx2


Resolution: 1.69→49.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.354 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22458 5681 10.1 %RANDOM
Rwork0.20659 ---
obs0.2084 50599 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.552 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---1.59 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.69→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 0 220 2800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222639
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9473570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28624125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43815453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.121512
X-RAY DIFFRACTIONr_chiral_restr0.1180.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021973
X-RAY DIFFRACTIONr_nbd_refined0.210.21284
X-RAY DIFFRACTIONr_nbtor_refined0.310.21855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.29
X-RAY DIFFRACTIONr_mcbond_it0.871.51627
X-RAY DIFFRACTIONr_mcangle_it1.40222575
X-RAY DIFFRACTIONr_scbond_it2.24131147
X-RAY DIFFRACTIONr_scangle_it3.2464.5995
LS refinement shellResolution: 1.69→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 286 -
Rwork0.231 2804 -
obs--85.38 %
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)
11.74550.035-0.85651.74350.15121.0545-0.0201-0.1499-0.12740.23050.0465-0.05380.10230.1184-0.0264-0.03640.015-0.0091-0.0380.0114-0.0595.98822.071616.3398
22.4721-0.3286-1.16080.7026-0.81965.699-0.15640.0319-0.0724-0.0401-0.0802-0.2416-0.02340.21660.2366-0.10390.01560.0035-0.03730.00210.001619.979820.37392.8462
31.04090.4559-0.29412.69970.62771.73010.1084-0.05890.27310.00960.08550.0236-0.27570.058-0.1939-0.0315-0.00940.0813-0.0884-0.0405-0.02067.071144.384716.4141
47.11230.6737-1.30782.02130.8434.5550.17880.64880.2045-0.72580.1826-0.2209-0.48390.2002-0.36140.0883-0.06560.157-0.12880.0158-0.087114.957645.6305-1.3435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1439 - 149
2X-RAY DIFFRACTION2CB206 - 23021 - 45
3X-RAY DIFFRACTION3BC4 - 14510 - 151
4X-RAY DIFFRACTION4DD206 - 23021 - 45

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