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- PDB-3acp: Crystal Structure of Yeast Rpn14, a Chaperone of the 19S Regulato... -

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Basic information

Entry
Database: PDB / ID: 3acp
TitleCrystal Structure of Yeast Rpn14, a Chaperone of the 19S Regulatory Particle of the Proteasome
ComponentsWD repeat-containing protein YGL004C
KeywordsCHAPERONE / WD40 domain / WD repeat
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 / MAD / Resolution: 2 Å
AuthorsKim, S. / Saeki, Y. / Suzuki, A. / Takagi, K. / Fukunaga, K. / Yamane, T. / Kato, K. / Tanaka, K. / Mizushima, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of yeast Rpn14, a chaperone of the 19S regulatory particle of the proteasome
Authors: Kim, S. / Saeki, Y. / Fukunaga, K. / Suzuki, A. / Takagi, K. / Yamane, T. / Tanaka, K. / Mizushima, T. / Kato, K.
History
DepositionJan 8, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein YGL004C


Theoretical massNumber of molelcules
Total (without water)46,4341
Polymers46,4341
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.581, 78.581, 110.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein WD repeat-containing protein YGL004C / WD40 protein


Mass: 46433.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
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.: 82 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1141.81
2
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, MgCl2, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.97914, 0.9794, 0.96417
Detector
TypeIDDetectorDate
Bruker DIP-60401CCDFeb 13, 2008
Bruker DIP-60402CCDFeb 13, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979141
30.97941
40.964171
ReflectionResolution: 2→39.28 Å / Num. obs: 26081 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 32.09 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10.1 / Num. measured all: 158070
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHELXphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.579 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1325 5.1 %RANDOM
Rwork0.2 ---
obs0.203 24720 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.58 Å2 / Biso mean: 39.994 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 82 3348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223328
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.9424505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7925416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60525.152165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8541516
X-RAY DIFFRACTIONr_chiral_restr0.1350.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212538
X-RAY DIFFRACTIONr_mcbond_it1.241.51583
X-RAY DIFFRACTIONr_mcangle_it2.20222560
X-RAY DIFFRACTIONr_scbond_it2.9493986
X-RAY DIFFRACTIONr_scangle_it4.7364.5913
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 106 -
Rwork0.273 1808 -
all-1914 -
obs--100 %

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