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- PDB-3vl1: Crystal structure of yeast Rpn14 -

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Basic information

Entry
Database: PDB / ID: 3vl1
TitleCrystal structure of yeast Rpn14
Components26S proteasome regulatory subunit RPN14
KeywordsCHAPERONE / Beta-Propeller / Rpt6
Function / homology
Function and homology information


proteasome regulatory particle assembly / protein folding chaperone / proteasome complex / ubiquitin-dependent protein catabolic process / nucleus / cytoplasm / cytosol
Similarity search - Function
: / WD domain, G-beta repeat / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKim, S. / Nishide, A. / Saeki, Y. / Takagi, K. / Tanaka, K. / Kato, K. / Mizushima, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: New crystal structure of the proteasome-dedicated chaperone Rpn14 at 1.6 A resolution
Authors: Kim, S. / Nishide, A. / Saeki, Y. / Takagi, K. / Tanaka, K. / Kato, K. / Mizushima, T.
History
DepositionNov 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN14
B: 26S proteasome regulatory subunit RPN14


Theoretical massNumber of molelcules
Total (without water)93,3162
Polymers93,3162
Non-polymers00
Water7,458414
1
A: 26S proteasome regulatory subunit RPN14


Theoretical massNumber of molelcules
Total (without water)46,6581
Polymers46,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 26S proteasome regulatory subunit RPN14


Theoretical massNumber of molelcules
Total (without water)46,6581
Polymers46,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-10 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.491, 141.443, 50.491
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 26S proteasome regulatory subunit RPN14 / Proteasome non-ATPase subunit 14


Mass: 46657.926 Da / Num. of mol.: 2 / Mutation: E384A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RPN14 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53196
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 1.92 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M NaCitrate pH4.5, 0.2M MgCl2, 10%(w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 90359 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.5
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.528 / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ACP

3acp


Resolution: 1.6→24.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.725 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23451 4505 5 %RANDOM
Rwork0.15394 ---
obs0.158 85676 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.03 Å2
2--0.19 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 0 414 6924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226913
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.941.9449424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.055913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48325.159345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.417151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7831535
X-RAY DIFFRACTIONr_chiral_restr0.0860.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.8251.54265
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.57726956
X-RAY DIFFRACTIONr_scbond_it17.80232648
X-RAY DIFFRACTIONr_scangle_it19.3424.52432
X-RAY DIFFRACTIONr_rigid_bond_restr14.99736913
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.597→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 311 -
Rwork0.223 6189 -
obs--95.35 %

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