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- PDB-1zx2: Crystal Structure of Yeast UBP3-associated Protein BRE5 -

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Basic information

Entry
Database: PDB / ID: 1zx2
TitleCrystal Structure of Yeast UBP3-associated Protein BRE5
ComponentsUBP3-associated protein BRE5
KeywordsSIGNALING PROTEIN / Ubp3 / deubiqutinate / NTF2
Function / homology
Function and homology information


Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / ribophagy / protein retention in Golgi apparatus / regulation of ER to Golgi vesicle-mediated transport / negative regulation of mitophagy / protein deubiquitination / stress granule assembly / P-body / cytoplasmic stress granule ...Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / ribophagy / protein retention in Golgi apparatus / regulation of ER to Golgi vesicle-mediated transport / negative regulation of mitophagy / protein deubiquitination / stress granule assembly / P-body / cytoplasmic stress granule / mRNA binding / mitochondrion / identical protein binding / 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 / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...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 / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Roll / Alpha Beta
Similarity search - Domain/homology
UBP3-associated protein BRE5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLi, K. / Zhao, K. / Ossareh-Nazari, B. / Da, G. / Dargemont, C. / Marmorstein, R.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural basis for interaction between the Ubp3 deubiquitinating enzyme and its Bre5 cofactor
Authors: Li, K. / Zhao, K. / Ossareh-Nazari, B. / Da, G. / Dargemont, C. / Marmorstein, R.
#1: Journal: Nat.Cell Biol. / Year: 2003
Title: Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23
Authors: Cohen, M. / Stutz, F. / Belgareh, N. / Haguenauer-Tsapis, R. / Dargemont, C.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 16, 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 / 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

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Assembly

Deposited unit
A: UBP3-associated protein BRE5
B: UBP3-associated protein BRE5


Theoretical massNumber of molelcules
Total (without water)33,8972
Polymers33,8972
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-16 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.909, 90.909, 194.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein UBP3-associated protein BRE5


Mass: 16948.256 Da / Num. of mol.: 2 / Fragment: NTF2-like domains (residues 1-146)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRE5 / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53741
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350, Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795, 0.9794, 0.9500, 0.9790
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
30.951
40.9791
ReflectionResolution: 2.1→50 Å / Num. obs: 28566 / % possible obs: 99.2 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 28.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 8.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→79.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.883 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21299 1445 5.1 %RANDOM
Rwork0.18833 ---
obs0.1896 27084 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.153 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 0 146 2247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222155
X-RAY DIFFRACTIONr_bond_other_d0.0090.021908
X-RAY DIFFRACTIONr_angle_refined_deg2.3961.9322914
X-RAY DIFFRACTIONr_angle_other_deg1.64234438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.815256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2260.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022354
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02478
X-RAY DIFFRACTIONr_nbd_refined0.2440.2425
X-RAY DIFFRACTIONr_nbd_other0.2740.22097
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1040.21338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6330.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4210.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6241.51294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04622104
X-RAY DIFFRACTIONr_scbond_it4.0893861
X-RAY DIFFRACTIONr_scangle_it6.6374.5810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 116
Rwork0.187 1951
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)
11.8702-0.2836-0.35840.7485-0.11740.3314-0.01180.0305-0.1874-0.06910.01440.03770.0462-0.1388-0.00260.0133-0.02620.01530.14890.03040.0552-5.5883491.101
21.0731-0.2756-0.11850.68610.08520.94860.0504-0.0717-0.0814-0.0536-0.0712-0.00130.00510.04630.02080.02710.01880.01490.11160.04140.051616.69634.27690.75
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1411 - 142
2X-RAY DIFFRACTION2BB2 - 1433 - 144

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