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- PDB-4a3t: yeast regulatory particle proteasome assembly chaperone Hsm3 -

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Basic information

Entry
Database: PDB / ID: 4a3t
Titleyeast regulatory particle proteasome assembly chaperone Hsm3
ComponentsDNA MISMATCH REPAIR PROTEIN HSM3
KeywordsCHAPERONE
Function / homology
Function and homology information


proteasome regulatory particle assembly / mismatch repair / nucleus / cytosol / cytoplasm
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 / Leucine-rich Repeat Variant / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA mismatch repair protein HSM3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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.H. / 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: DNA MISMATCH REPAIR PROTEIN HSM3


Theoretical massNumber of molelcules
Total (without water)112,0262
Polymers112,0262
Non-polymers00
Water10,539585
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-16.3 kcal/mol
Surface area39970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.070, 94.950, 129.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA MISMATCH REPAIR PROTEIN HSM3 / / ENHANCED SPONTANEOUS MUTABILITY PROTEIN 3


Mass: 56012.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P38348
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.4 Å3/Da / Density % sol: 48.24 % / Description: NONE
Crystal growpH: 5.5 / Details: 20% PEG 4000, 0.2 M MALATE IMIDAZOLE, PH 5.5.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.992
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.1→30.7 Å / Num. obs: 62865 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.86 % / Biso Wilson estimate: 26.95 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.99
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.18 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→30.75 Å / Cor.coef. Fo:Fc: 0.9404 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. RESTRAINT LIBRARIES. NUMBER OF LIBRARIES USED: 7
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 3136 5 %RANDOM
Rwork0.1846 ---
obs0.1863 62736 --
Displacement parametersBiso mean: 32.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.9536 Å20 Å20 Å2
2--0.6468 Å20 Å2
3---2.3067 Å2
Refine analyzeLuzzati coordinate error obs: 0.235 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7304 0 0 585 7889
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017467HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0310116HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2709SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes218HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1044HARMONIC5
X-RAY DIFFRACTIONt_it7467HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion17.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion979SEMIHARMONIC5
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_contact9450SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1992 227 4.99 %
Rwork0.1864 4321 -
all0.187 4548 -
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)
10.22630.0244-0.17810.6219-0.46160.50410.0277-0.0271-0.01060.0179-0.0621-0.0492-0.02020.07860.0343-0.0357-0.0043-0.0221-0.0393-0.0232-0.058232.51552.59910.3563
20.19660.11360.20180.38620.33020.48050.0222-0.04110.01060.0558-0.02870.01960.0294-0.09190.0065-0.04560.00230.0283-0.02230.0113-0.041949.2979-2.976-1.6073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 8-21 OR RESID 27-42 OR RESID 51-64 OR RESID 72-418 OR RESID 424-465
2X-RAY DIFFRACTION2CHAIN B AND RESID 7-465

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