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- PDB-4a3v: yeast regulatory particle proteasome assembly chaperone Hsm3 in c... -

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Basic information

Entry
Database: PDB / ID: 4a3v
Titleyeast regulatory particle proteasome assembly chaperone Hsm3 in complex with Rpt1 C-terminal fragment
Components
  • 26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG
  • DNA MISMATCH REPAIR PROTEIN HSM3
  • LINKER
KeywordsCHAPERONE/ATP BINDING PROTEIN / CHAPERONE-ATP BINDING PROTEIN COMPLEX / 19S
Function / homology
Function and homology information


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 / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...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 / 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 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mismatch repair / Neutrophil degranulation / 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 ...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 / 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 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
AuthorsRichet, N. / Barrault, M.B. / Godart, C. / Murciano, B. / Le Tallec, B. / Rousseau, E. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Guerois, R. ...Richet, N. / Barrault, M.B. / Godart, C. / Murciano, B. / Le Tallec, B. / Rousseau, E. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Guerois, R. / Peyroche, A. / Ochsenbein, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Dual Functions of the Hsm3 Protein in Chaperoning and Scaffolding Regulatory Particle Subunits During the Proteasome Assembly.
Authors: Barrault, M.B. / Richet, N. / Godard, C. / Murciano, B. / Le Tallec, B. / Rousseau, E. / Legrand, P. / Charbonnier, J.B. / Le Du, M. / Guerois, R. / Ochsenbein, F. / Peyroche, A.
History
DepositionOct 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: LINKER


Theoretical massNumber of molelcules
Total (without water)136,3165
Polymers136,3165
Non-polymers00
Water00
1
A: DNA MISMATCH REPAIR PROTEIN HSM3
B: 26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)67,7232
Polymers67,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-5.9 kcal/mol
Surface area24360 Å2
MethodPISA
2
C: DNA MISMATCH REPAIR PROTEIN HSM3
D: 26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)67,7232
Polymers67,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-4.5 kcal/mol
Surface area24230 Å2
MethodPISA
3
E: LINKER


  • defined by author&software
  • 869 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8691
Polymers8691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.660, 186.660, 373.770
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 / HSM3 / ENHANCED SPONTANEOUS MUTABILITY PROTEIN 3


Mass: 57088.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P38348
#2: Protein 26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG / RPT1-CTER / PROTEIN CIM5 / TAT-BINDING HOMOLOG 3


Mass: 10635.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P33299
#3: Protein/peptide LINKER


Mass: 869.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHAIN E IS BELIEVED TO BE MADE OF RESIDUES FROM THE C-TERMINUS OF EITHER CHAIN A OR C, BUT THE IDENTITY IS UNCERTAIN.
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21

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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

CrystalDescription: NONE
Crystal growpH: 7.5 / Details: 5M SODIUM FORMATE, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.8→60 Å / Num. obs: 38668 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 15.6 % / Biso Wilson estimate: 148.95 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.32
Reflection shellResolution: 3.8→3.91 Å / Redundancy: 11.71 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.32 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→58.35 Å / Cor.coef. Fo:Fc: 0.9529 / Cor.coef. Fo:Fc free: 0.9466 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1933 5 %RANDOM
Rwork0.1904 ---
obs0.1913 38668 --
Displacement parametersBiso mean: 225.22 Å2
Baniso -1Baniso -2Baniso -3
1-17.6129 Å20 Å20 Å2
2--17.6129 Å20 Å2
3----35.2257 Å2
Refine analyzeLuzzati coordinate error obs: 1.655 Å
Refinement stepCycle: LAST / Resolution: 3.8→58.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8722 0 0 0 8722
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018870HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2311999HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3199SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes246HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1247HARMONIC5
X-RAY DIFFRACTIONt_it8870HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion23.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1166SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11071SEMIHARMONIC4
LS refinement shellResolution: 3.8→3.9 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2573 146 4.99 %
Rwork0.2492 2780 -
all0.2497 2926 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.82581.11620.656913.8794-6.529630.5761-0.26261.06050.3811-1.35480.93150.47980.722-1.3682-0.66890.74510.5049-0.27740.73660.3026-0.4791-70.3137-37.43556.2944
2-0.2358-0.01152.77262.47041.13973.75910.1914-0.312-0.2669-0.82990.5937-0.0968-0.7404-0.5288-0.78510.74720.66690.2760.31160.35520.0207-66.4691-25.625418.3997
3-0.40290.23261.57150.4029-1.793300.228-0.0843-0.0223-0.10120.0825-0.17460.0527-0.2782-0.31050.54720.46940.29690.0066-0.13080.2791-56.457-29.322842.413
40.9158-0.84710.78790.187-0.384300.2456-0.0177-0.47090.11550.3775-0.1241-0.5280.032-0.62310.43780.40430.03240.1232-0.26380.2495-49.7165-41.870258.6059
5-0.52310.4544-2.12160.69910.10570.1217-0.27070.25750.24990.26710.1181-0.05270.2912-0.02110.15260.35050.4477-0.36340.363-0.31330.2227-40.2918-62.268552.6848
61.3592-1.11230.87561.2985-4.04210-0.2891-0.05240.4449-0.2198-0.0148-0.04710.9215-0.21290.3040.22780.5626-0.16360.2191-0.34210.3211-33.4138-75.877642.3619
75.9483-3.1175-2.7678-5.5825-0.84022.7746-0.63820.32970.43970.28370.55560.05280.5642-0.0320.08260.10770.2685-0.14640.5664-0.34490.2478-35.9286-70.61832.4261
80.5321-0.17190.4997-0.3741-1.46150.54530.3443-0.149-0.6766-0.14320.5278-0.0915-0.6224-0.2899-0.87210.25310.397-0.15230.19090.04360.3298-69.3398-48.81742.591
916.51172.4489-15.874838.97744.244830.1292-0.2795-0.62510.65411.6668-0.1447-1.6405-1.74050.23670.42421.43840.08140.82870.0326-0.21951.2153-26.3869-28.789220.4371
1015.046518.0612-1.871621.07436.071824.04141.2641-0.73981.54811.4242-0.81381.1737-1.9533-0.5944-0.45030.05010.030.5934-0.1115-0.17861.2159-19.78-35.00726.1886
11-1.38461.51510.39412.2110.055800.0790.55420.21960.27360.4645-0.09520.2777-0.3859-0.5435-0.27840.27360.34420.80970.24420.4894-25.0954-57.6755-5.7857
124.8837-0.58411.8946-2.3024-0.623200.08130.19420.3333-0.15420.0893-0.37850.26-0.4659-0.1706-0.15090.18120.17791.04380.00440.0463-36.0488-76.2272-6.7072
131.0528-0.6078-1.4759-1.05280.10670-0.32750.570.21940.5260.24640.00410.1410.04340.0811-0.09010.14110.04861.0166-0.23780.004-56.4745-74.05053.9078
1413.5371-2.4296-1.8796-7.317-2.69760.4231-0.13090.5107-0.69260.82870.1438-0.7951-0.6402-0.4825-0.0129-0.23990.1880.21840.836-0.24610.134-70.5411-65.936712.7051
153.0911-3.57754.28923.1194-1.01770.2075-0.6450.4472-0.11870.79170.1859-0.4011-0.4963-0.52250.45920.18460.4324-0.17810.5101-0.04080.167-65.6381-55.700613.3367
16-0.11560.8094-1.12662.4979-0.05690.01630.04890.2059-0.02820.12170.4704-0.2632-0.1003-0.2456-0.5194-0.12410.3644-0.04320.8591-0.1830.1482-27.8247-65.856816.1209
173.2279-2.2096-10.93563.78584.70990.04420.133-0.2207-0.2448-0.20880.1092-0.0948-0.57060.1812-0.24221.2081-0.2369-0.24340.36240.2399-0.4677-76.97-59.0635.2829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4 - 45)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46 - 137)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 138 - 257)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 258 - 316)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 317 - 404)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 405 - 418)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 426 - 465)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 377 - 455)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 8 - 45)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 46 - 137)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 138 - 257)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 258 - 316)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 317 - 404)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 405 - 418)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 419 - 465)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 378 - 454)
17X-RAY DIFFRACTION17(CHAIN E AND RESID 483 - 492)

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