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- PDB-2dzn: Crystal structure analysis of yeast Nas6p complexed with the prot... -

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Basic information

Entry
Database: PDB / ID: 2dzn
TitleCrystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3
Components
  • 26S protease regulatory subunit 6B homolog
  • Probable 26S proteasome regulatory subunit p28
KeywordsPROTEIN BINDING / ankyrin repeats / a-helical domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


proteasome regulatory particle binding / proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome regulatory particle binding / proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Ub-specific processing proteases / protein folding chaperone / proteasome complex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Ankyrin repeat-containing domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / Ankyrin repeat / Ankyrin repeats (3 copies) ...: / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Ankyrin repeat-containing domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / Ankyrin repeat / Ankyrin repeats (3 copies) / ATPase family associated with various cellular activities (AAA) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / ATPase, AAA-type, core / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome regulatory subunit 6B homolog / Probable 26S proteasome regulatory subunit p28
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYokoyama, S. / Padmanabhan, B. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome
Authors: Nakamura, Y. / Umehara, T. / Tanaka, A. / Horikoshi, M. / Padmanabhan, B. / Yokoyama, S.
History
DepositionSep 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable 26S proteasome regulatory subunit p28
B: 26S protease regulatory subunit 6B homolog
C: Probable 26S proteasome regulatory subunit p28
D: 26S protease regulatory subunit 6B homolog
E: Probable 26S proteasome regulatory subunit p28
F: 26S protease regulatory subunit 6B homolog


Theoretical massNumber of molelcules
Total (without water)104,5706
Polymers104,5706
Non-polymers00
Water8,503472
1
A: Probable 26S proteasome regulatory subunit p28
B: 26S protease regulatory subunit 6B homolog


Theoretical massNumber of molelcules
Total (without water)34,8572
Polymers34,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-7 kcal/mol
Surface area12560 Å2
MethodPISA
2
C: Probable 26S proteasome regulatory subunit p28
D: 26S protease regulatory subunit 6B homolog


Theoretical massNumber of molelcules
Total (without water)34,8572
Polymers34,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-4 kcal/mol
Surface area12610 Å2
MethodPISA
3
E: Probable 26S proteasome regulatory subunit p28
F: 26S protease regulatory subunit 6B homolog


Theoretical massNumber of molelcules
Total (without water)34,8572
Polymers34,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.376, 100.220, 72.203
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable 26S proteasome regulatory subunit p28 / NAS6P / Proteasome non-ATPase subunit 6


Mass: 25648.268 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / References: UniProt: P50086
#2: Protein 26S protease regulatory subunit 6B homolog / RPT3 / Protein YNT1 / TAT-binding homolog 2


Mass: 9208.535 Da / Num. of mol.: 3 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33298
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG6K, MES, pH 6.50, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 43936 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.203 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GANKYRIN

Resolution: 2.2→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4296 -RANDOM
Rwork0.197 ---
obs0.197 42627 98.1 %-
Displacement parametersBiso mean: 42.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6874 0 0 472 7346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 2.2→2.26 Å /
RfactorNum. reflection
Rfree0.3 321
Rwork0.25 -

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