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- PDB-3vlf: Crystal structure of yeast proteasome interacting protein -

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Basic information

Entry
Database: PDB / ID: 3vlf
TitleCrystal structure of yeast proteasome interacting protein
Components
  • 26S protease regulatory subunit 7 homolog
  • DNA mismatch repair protein HSM3
KeywordsCHAPERONE/PROTEIN BINDING / HEAT REPEAT / CHAPERONE / CHAPERONE-PROTEIN BINDING complex
Function / homology
Function and homology information


proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Proteasome 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Proteasome 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 / 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 / mismatch repair / Neutrophil degranulation / protein folding chaperone / proteasome complex / positive regulation of protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Leucine-rich Repeat Variant - #50 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #580 / DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / : / 26S proteasome regulatory subunit 7, OB domain / : / Helicase, Ruva Protein; domain 3 - #60 ...Leucine-rich Repeat Variant - #50 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #580 / DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / : / 26S proteasome regulatory subunit 7, OB domain / : / Helicase, Ruva Protein; domain 3 - #60 / Leucine-rich Repeat Variant / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome regulatory subunit 7 homolog / DNA mismatch repair protein HSM3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsTakagi, K. / Kim, S. / Kato, K. / Tanaka, K. / Saeki, Y. / Mizushima, T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for specific recognition of Rpt1, an ATPase subunit of the 26S proteasome, by a proteasome-dedicated chaperone Hsm3
Authors: Takagi, K. / Kim, S. / Yukii, H. / Ueno, M. / Morishita, R. / Endo, Y. / Kato, K. / Tanaka, K. / Saeki, Y. / Mizushima, T.
History
DepositionDec 1, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA mismatch repair protein HSM3
B: 26S protease regulatory subunit 7 homolog
C: DNA mismatch repair protein HSM3
D: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)137,0864
Polymers137,0864
Non-polymers00
Water00
1
A: DNA mismatch repair protein HSM3
B: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)68,5432
Polymers68,5432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA mismatch repair protein HSM3
D: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)68,5432
Polymers68,5432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-5 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.282, 187.282, 379.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DNA mismatch repair protein HSM3 / Enhanced spontaneous mutability protein 3


Mass: 58241.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HSM3, YBR272C, YBR1740 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P38348
#2: Protein 26S protease regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


Mass: 10301.319 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP residues 381-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RPT1, CIM5, YTA3, YKL145W / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P33299
Has protein modificationY

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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: 7.01 Å3/Da / Density % sol: 82.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1M sodium chloride, 0.5% PEG 3350, 0.8M lithium sulfate, 0.1M N-(2-acetamido) iminodiacetic acid, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Oct 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 39787 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.1
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 7.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VLD

3vld


Resolution: 3.8→30 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 1952 4.9 %RANDOM
Rwork0.2505 ---
obs0.2505 39285 --
Solvent computationBsol: 122.039 Å2
Displacement parametersBiso mean: 163.3521 Å2
Refinement stepCycle: LAST / Resolution: 3.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8594 0 0 0 8594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006402
X-RAY DIFFRACTIONc_angle_deg0.81161
X-RAY DIFFRACTIONc_mcbond_it8.73315
X-RAY DIFFRACTIONc_scbond_it12.08320
X-RAY DIFFRACTIONc_mcangle_it13.5420
X-RAY DIFFRACTIONc_scangle_it17.55425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.940.38651950.36893639383499.4
3.94-4.090.351860.32623664385099.5
4.09-4.280.34692080.30333652386099.6
4.28-4.50.33161800.28113682386299.6
4.5-4.780.26761750.25213699387499.5
4.78-5.150.26151960.22683702389899.5
5.15-5.670.26121830.24293747393099.7
5.67-6.480.32862100.28973735394599.6
6.48-8.140.31822090.24463806401599.8
8.14-300.20872100.20824007421799.6

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