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- PDB-3whj: Crystal structure of Nas2 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3whj
TitleCrystal structure of Nas2 N-terminal domain
ComponentsProbable 26S proteasome regulatory subunit p27
KeywordsCHAPERONE / Proteasome assembly chaperone
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
Helix Hairpins - #1710 / 26S Proteasome non-ATPase regulatory subunit 9 / Nas2, N-terminal / Nas2 N_terminal domain / Helix Hairpins / PDZ domain / Helix non-globular / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Special
Similarity search - Domain/homology
: / Probable 26S proteasome regulatory subunit p27
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)14,6168
Polymers13,8621
Non-polymers7547
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable 26S proteasome regulatory subunit p27
hetero molecules

A: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,23216
Polymers27,7232
Non-polymers1,50814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_575x,x-y+2,-z+1/61
Buried area2900 Å2
ΔGint-31 kcal/mol
Surface area13880 Å2
MethodPISA
3
A: Probable 26S proteasome regulatory subunit p27
hetero molecules

A: Probable 26S proteasome regulatory subunit p27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,23216
Polymers27,7232
Non-polymers1,50814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2070 Å2
ΔGint-18 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.59, 64.59, 149.76
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

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Components

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


Mass: 13861.723 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.9M sodium acetate trihydrate, 0.1M HEPES (pH 8.5), 50mM cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 23223 / Num. obs: 23180 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 45.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1106 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.35 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1176 5.1 %RANDOM
Rwork0.159 ---
obs0.161 21760 99.35 %-
all-21760 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.133 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å2-1.47 Å20 Å2
2---1.47 Å20 Å2
3---4.77 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 15 97 1004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019908
X-RAY DIFFRACTIONr_bond_other_d0.0010.02890
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9851222
X-RAY DIFFRACTIONr_angle_other_deg0.95832048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53626.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65515183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.898154
X-RAY DIFFRACTIONr_chiral_restr0.120.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02192
X-RAY DIFFRACTIONr_rigid_bond_restr3.44231794
X-RAY DIFFRACTIONr_sphericity_free46.124541
X-RAY DIFFRACTIONr_sphericity_bonded21.49751853
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 90 -
Rwork0.157 1551 -
obs--99.45 %

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