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- PDB-1g4a: CRYSTAL STRUCTURES OF THE HSLVU PEPTIDASE-ATPASE COMPLEX REVEAL A... -

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Basic information

Entry
Database: PDB / ID: 1g4a
TitleCRYSTAL STRUCTURES OF THE HSLVU PEPTIDASE-ATPASE COMPLEX REVEAL AN ATP-DEPENDENT PROTEOLYSIS MECHANISM
Components
  • ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
  • ATP-DEPENDENT PROTEASE HSLV
KeywordsCHAPERONE/HYDROLASE / HSLVU / PEPTIDASE-ATPASE COMPLEX / CHAPERONE-HYDROLASE COMPLEX
Function / homology
Function and homology information


HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat ...HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Aminohydrolase, N-terminal nucleophile (Ntn) domain ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Helicase, Ruva Protein; domain 3 / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 4-Layer Sandwich / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsWang, J. / Song, J.J. / Franklin, M.C. / Kamtekar, S. / Im, Y.J. / Rho, S.H. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Eom, S.H.
Citation
Journal: Structure / Year: 2001
Title: Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism.
Authors: Wang, J. / Song, J.J. / Franklin, M.C. / Kamtekar, S. / Im, Y.J. / Rho, S.H. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Eom, S.H.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Purification and Characterization of the Heat Shock Proteins HslV and HslU that form a New ATP-Dependent Protease in Escherichia Coli
Authors: Yoo, S.J. / Seol, J.H. / Shin, D.H. / Rohrwild, M. / Kang, M.S. / Tanaka, K. / Goldberg, A.L. / Chung, C.H.
#2: Journal: Nature / Year: 2000
Title: The Structuers of HslU and the ATP-Dependent Protease HslU-HslV.
Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
History
DepositionOct 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT PROTEASE HSLV
A: ATP-DEPENDENT PROTEASE HSLV
D: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,0888
Polymers175,2666
Non-polymers8222
Water00
1
E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT PROTEASE HSLV
A: ATP-DEPENDENT PROTEASE HSLV
D: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT PROTEASE HSLV
A: ATP-DEPENDENT PROTEASE HSLV
D: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT PROTEASE HSLV
A: ATP-DEPENDENT PROTEASE HSLV
D: ATP-DEPENDENT PROTEASE HSLV
C: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,26524
Polymers525,79818
Non-polymers2,4676
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)169.995, 169.995, 161.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU / HEAT SHOCK LOCUS HSLU ATPASE


Mass: 49659.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H5
#2: Protein
ATP-DEPENDENT PROTEASE HSLV / HEAT SHOCK LOCUS HSLV PEPTIDASE


Mass: 18986.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7B8, EC: 3.4.99.-
#3: Chemical ChemComp-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP


Mass: 411.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O9P2

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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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growMethod: vapor diffusion / Details: dADP-HslU-HslV, VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mM1dropMgCl2
40.5 mMEDTA1drop
51 mMdithiothreitol1drop
610 %glycerol1drop
710 %ethylene glycol1reservoir
820 mM1reservoirMgCl2
92 mMdithiothreitol1reservoir
101 mMEDTA1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 85 Å / Num. obs: 46551 / % possible obs: 86 % / Rmerge(I) obs: 0.131

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 3→85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 145156.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 4647 10 %RANDOM IN TWINNED SPACE GROUP P622 TWINNING OPERATION : (-H,-K,L)
Rwork0.2574 ---
obs0.2574 46551 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.98 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso mean: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å24.27 Å20 Å2
2--2.61 Å20 Å2
3----5.21 Å2
Refinement stepCycle: LAST / Resolution: 3→85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10868 0 52 0 10920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
Num. reflection% reflection
Rfree779 10.8 %
Rwork6401 -
obs-80.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DADP.PARDADP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
% reflection Rfree: 10.8 %

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