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- PDB-3whl: Crystal structure of Nas2 N-terminal domain complexed with PAN-Rp... -

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Basic information

Entry
Database: PDB / ID: 3whl
TitleCrystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera
Components
  • Probable 26S proteasome regulatory subunit p27
  • Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
KeywordsHYDROLASE/CHAPERONE / Four-helix bundle / Proteasome ATPase subunit / Proteasome assembly chaperone / ATP Binding / HYDROLASE-CHAPERONE complex
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome regulatory particle assembly ...proteasome-activating nucleotidase complex / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome regulatory particle assembly / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / protein unfolding / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1710 / 26S Proteasome non-ATPase regulatory subunit 9 / Nas2, N-terminal / Nas2 N_terminal domain / Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Helix Hairpins / AAA ATPase, AAA+ lid domain ...Helix Hairpins - #1710 / 26S Proteasome non-ATPase regulatory subunit 9 / Nas2, N-terminal / Nas2 N_terminal domain / Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Helix Hairpins / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / PDZ domain / Helix non-globular / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Special / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome regulatory subunit 6A / Probable 26S proteasome regulatory subunit p27 / Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsSatoh, T. / Saeki, Y. / Hiromoto, T. / Wang, Y.-H. / Uekusa, Y. / Yagi, H. / Yoshihara, H. / Yagi-Utsumi, M. / Mizushima, T. / Tanaka, K. / Kato, K.
CitationJournal: Structure / Year: 2014
Title: Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Authors: Satoh, T. / Saeki, Y. / Hiromoto, T. / Wang, Y.H. / Uekusa, Y. / Yagi, H. / Yoshihara, H. / Yagi-Utsumi, M. / Mizushima, T. / Tanaka, K. / Kato, K.
History
DepositionAug 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
B: Probable 26S proteasome regulatory subunit p27
C: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
D: Probable 26S proteasome regulatory subunit p27
E: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
F: Probable 26S proteasome regulatory subunit p27
G: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
H: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,56912
Polymers175,5408
Non-polymers2,0294
Water0
1
A: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
B: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3923
Polymers43,8852
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-13 kcal/mol
Surface area16860 Å2
MethodPISA
2
C: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
D: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3923
Polymers43,8852
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-14 kcal/mol
Surface area16810 Å2
MethodPISA
3
E: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
F: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3923
Polymers43,8852
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-12 kcal/mol
Surface area16520 Å2
MethodPISA
4
G: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
H: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3923
Polymers43,8852
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-13 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.63, 110.63, 251.94
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A / PAN / Proteasomal ATPase / Proteasome regulatory ATPase / Proteasome regulatory particle / Tat- ...PAN / Proteasomal ATPase / Proteasome regulatory ATPase / Proteasome regulatory particle / Tat-binding protein homolog 1 / TBP-1


Mass: 30023.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fusion protein of residues 125-309 FROM Proteasome-activating nucleotidase (PAN, UNP Q8U4H3), linker (EF), and residues 356-434 from 26S protease regulatory subunit 6A (Rpt5, UNP P33297).
Source: (gene. exp.) Pyrococcus furiosus (archaea), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: DSM 3638, S288c / Gene: pan, PF0115, O3258, RPT5, YOR117W, YOR3258W, YTA1 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q8U4H3, UniProt: P33297
#2: Protein
Probable 26S proteasome regulatory subunit p27 / Proteasome non-ATPase subunit 2


Mass: 13861.723 Da / Num. of mol.: 4 / Fragment: N-terminal domain, UNP residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NAS2, YIL007C / Plasmid: pCold-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: P40555
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 8% PEG 6000, 0.1M MES (pH6.0), 80mM MgCl2, VAPOR DIFFUSION, SITTING 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 MX-225 / Detector: CCD / Date: Jan 30, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 15872 / Num. obs: 15849 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 110.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 28.1
Reflection shellResolution: 4→4.07 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 5 / Num. unique all: 787 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WHK

3whk


Resolution: 4→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.764 / SU ML: 0.47 / σ(F): 0.65 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 768 4.97 %
Rwork0.233 --
all0.235 15461 -
obs0.235 15461 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 248.44 Å2 / Biso mean: 148.2997 Å2 / Biso min: 90.23 Å2
Refinement stepCycle: LAST / Resolution: 4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10209 0 124 0 10333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310480
X-RAY DIFFRACTIONf_angle_d0.87614166
X-RAY DIFFRACTIONf_dihedral_angle_d17.0394013
X-RAY DIFFRACTIONf_chiral_restr0.051649
X-RAY DIFFRACTIONf_plane_restr0.0031822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.0005-4.30650.33641650.2616284499
4.3065-4.73460.30461800.2331286999
4.7346-5.40780.29921450.23372931100
5.4078-6.76870.3351400.2718295499
6.7687-19.94010.23251380.2094309599

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