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- PDB-4o06: 1.15A Resolution Structure of the Proteasome Assembly Chaperone N... -

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Basic information

Entry
Database: PDB / ID: 4o06
Title1.15A Resolution Structure of the Proteasome Assembly Chaperone Nas2 PDZ Domain
ComponentsProbable 26S proteasome regulatory subunit p27
KeywordsCHAPERONE / Nas2 / Proteasome / PDZ domain
Function / homology
Function and homology information


proteasome regulatory particle assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin ...proteasome regulatory particle assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / nucleus / cytoplasm / cytosol
Similarity search - Function
26S Proteasome non-ATPase regulatory subunit 9 / Nas2, N-terminal / Nas2 N_terminal domain / PDZ domain / Pdz3 Domain / PDZ domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Probable 26S proteasome regulatory subunit p27
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Singh, C.R. / Chowdhury, W.Q. / Geanes, E. / Roelofs, J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: 1.15 angstrom resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain.
Authors: Singh, C.R. / Lovell, S. / Mehzabeen, N. / Chowdhury, W.Q. / Geanes, E.S. / Battaile, K.P. / Roelofs, J.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9353
Polymers11,6441
Non-polymers2902
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.968, 39.968, 115.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein Probable 26S proteasome regulatory subunit p27 / Proteasome non-ATPase subunit 2


Mass: 11644.451 Da / Num. of mol.: 1 / Fragment: PDZ Domain (residues 126-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NAS2, YIL007C / Plasmid: pGR608 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P40555
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 10% (w/v) PEG 2000MME, 100 mM sodium acetate, 200 mM ammonium sulfate, pH 5.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→39.97 Å / Num. all: 33545 / Num. obs: 33545 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 3.4 / Num. measured all: 27697 / Num. unique all: 1574 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.8data scaling
PHENIXdev_1563refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLE

3rle


Resolution: 1.15→32.895 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.23 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1698 5.07 %RANDOM
Rwork0.1716 ---
obs0.1727 33494 97.38 %-
all-33494 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.27 Å2 / Biso mean: 17.9684 Å2 / Biso min: 7.91 Å2
Refinement stepCycle: LAST / Resolution: 1.15→32.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms779 0 13 98 890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012834
X-RAY DIFFRACTIONf_angle_d1.3561137
X-RAY DIFFRACTIONf_chiral_restr0.103132
X-RAY DIFFRACTIONf_plane_restr0.012148
X-RAY DIFFRACTIONf_dihedral_angle_d14.754331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.18380.24981170.21832530264795
1.1838-1.22210.2251420.17232534267695
1.2221-1.26570.17931310.15912548267996
1.2657-1.31640.20781510.1512574272596
1.3164-1.37630.1951430.1422590273397
1.3763-1.44890.18461470.13942587273497
1.4489-1.53970.20141220.13852660278298
1.5397-1.65850.17081400.14142644278498
1.6585-1.82540.18761520.14922682283499
1.8254-2.08950.15811540.15552703285799
2.0895-2.63240.18781430.173727772920100
2.6324-32.90830.2111560.196429673123100

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