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- PDB-4jpo: 5A resolution structure of Proteasome Assembly Chaperone Hsm3 in ... -

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Basic information

Entry
Database: PDB / ID: 4jpo
Title5A resolution structure of Proteasome Assembly Chaperone Hsm3 in complex with a C-terminal fragment of Rpt1
Components
  • 26S protease regulatory subunit 7 homolog
  • DNA mismatch repair protein HSM3
KeywordsCHAPERONE/HYDROLASE / Hsm3 / Chaperone / Proteasome / Protein Complex / CHAPERONE-HYDROLASE 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 / cytosol / cytoplasm
Similarity search - Function
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 / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site ...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 / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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
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 / molecular replacement / Resolution: 5 Å
AuthorsLovell, S. / Battaile, K.P. / Singh, R. / Roelofs, J.
CitationJournal: Nature / Year: 2013
Title: Reconfiguration of the proteasome during chaperone-mediated assembly.
Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan ...Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan Cheng / Daniel Finley /
Abstract: The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting ...The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting into pockets of the α-ring. Rpt ring assembly is mediated by four chaperones, each binding a distinct Rpt subunit. Here we report that the base subassembly of the Saccharomyces cerevisiae proteasome, which includes the Rpt ring, forms a high-affinity complex with the CP. This complex is subject to active dissociation by the chaperones Hsm3, Nas6 and Rpn14. Chaperone-mediated dissociation was abrogated by a non-hydrolysable ATP analogue, indicating that chaperone action is coupled to nucleotide hydrolysis by the Rpt ring. Unexpectedly, synthetic Rpt tail peptides bound α-pockets with poor specificity, except for Rpt6, which uniquely bound the α2/α3-pocket. Although the Rpt6 tail is not visualized within an α-pocket in mature proteasomes, it inserts into the α2/α3-pocket in the base-CP complex and is important for complex formation. Thus, the Rpt-CP interface is reconfigured when the lid complex joins the nascent proteasome to form the mature holoenzyme.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: 26S protease regulatory subunit 7 homolog
D: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)136,6464
Polymers136,6464
Non-polymers00
Water00
1
A: DNA mismatch repair protein HSM3


Theoretical massNumber of molelcules
Total (without water)56,6861
Polymers56,6861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA mismatch repair protein HSM3


Theoretical massNumber of molelcules
Total (without water)56,6861
Polymers56,6861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)11,6371
Polymers11,6371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)11,6371
Polymers11,6371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: DNA mismatch repair protein HSM3
C: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)68,3232
Polymers68,3232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-4 kcal/mol
Surface area23680 Å2
MethodPISA
6
B: DNA mismatch repair protein HSM3
D: 26S protease regulatory subunit 7 homolog


Theoretical massNumber of molelcules
Total (without water)68,3232
Polymers68,3232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-5 kcal/mol
Surface area23930 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-19 kcal/mol
Surface area45490 Å2
MethodPISA
8
A: DNA mismatch repair protein HSM3
B: DNA mismatch repair protein HSM3
C: 26S protease regulatory subunit 7 homolog
D: 26S protease regulatory subunit 7 homolog

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


Theoretical massNumber of molelcules
Total (without water)273,2938
Polymers273,2938
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area16790 Å2
ΔGint-60 kcal/mol
Surface area86860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.299, 185.299, 357.382
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 56685.719 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: pJR89 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P38348
#2: Protein 26S protease regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


Mass: 11637.442 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 379-467
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: pJR89 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P33299

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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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 3M Sodium Formate, 100 mM Bis-Tris, 10mM Calcium Chloride, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5→160.474 Å / Num. all: 16422 / Num. obs: 16422 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.1
Reflection shellResolution: 5→5.59 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4550 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FP7

4fp7


Resolution: 5→46.87 Å / Cor.coef. Fo:Fc: 0.9254 / Cor.coef. Fo:Fc free: 0.9109 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: B-factors were set to the value determined from the Wilson plot for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 829 5.07 %RANDOM
Rwork0.2528 ---
obs0.2538 16355 99.94 %-
all-16355 --
Displacement parametersBiso max: 273 Å2 / Biso mean: 273 Å2 / Biso min: 273 Å2
Baniso -1Baniso -2Baniso -3
1-5.0616 Å20 Å20 Å2
2--5.0616 Å20 Å2
3----10.1232 Å2
Refine analyzeLuzzati coordinate error obs: 2.055 Å
Refinement stepCycle: LAST / Resolution: 5→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8391 0 0 0 8391
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4059SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1207HARMONIC5
X-RAY DIFFRACTIONt_it8532HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1133SEMIHARMONIC5
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_contact10692SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8532HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg11551HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion3.51
LS refinement shellResolution: 5→5.34 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3274 152 5.27 %
Rwork0.2997 2733 -
all0.3012 2885 -
obs-2733 99.94 %

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