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- PDB-1g4b: CRYSTAL STRUCTURES OF THE HSLVU PEPTIDASE-ATPASE COMPLEX REVEAL A... -

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Basic information

Entry
Database: PDB / ID: 1g4b
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 / cytoplasm / cytosol
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 7 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV


Theoretical massNumber of molelcules
Total (without water)274,5858
Polymers274,5858
Non-polymers00
Water00
1
E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV

E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV

E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV


Theoretical massNumber of molelcules
Total (without water)823,75624
Polymers823,75624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)173.376, 173.376, 254.411
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.: 4
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.-

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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: 4.02 Å3/Da / Density % sol: 69.39 %
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
127 mg/mlprotein1drop
20.1 MMES1reservoir
31.5 M1reservoirNaAc
420 mMTris-HCl1drop
55 mM1dropMgCl2
60.5 mMEDTA1drop
71 mMdithiothreitol1drop
810 %glycerol1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 7 Å / Lowest resolution: 80 Å / Num. obs: 6489 / % possible obs: 87 % / Rmerge(I) obs: 0.201

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 7→10 Å
Details: There are approximately 200 close contacts present within the asymmetric unit and 300 close contacts among crystal symmetry related subunits. These contacts resulted from a standard rigid- ...Details: There are approximately 200 close contacts present within the asymmetric unit and 300 close contacts among crystal symmetry related subunits. These contacts resulted from a standard rigid-body refinement during which contact penalty was not included. These contacts may imply domain motions with each subunit, which is yet to be resolved at higher resolutions. RIGID-BODY REFINEMENT ONLY WITH ONE BODY PER SUBUNIT. COORDINATES FROM TWINNED DATA RIGID-BODY REFINEMENT. TWINNING OPERATOR= -H,-K,L TWINNING FRACTION= .500. REFINEMENT RESOLUTION: 10 - 7 A. STARTING TWINNED R= 0.4447 TWINNED FREE_R= 0.4607. FINAL TWINNED R= 0.4008 TWINNED FREE_R= 0.4322. TARGET= TWIN_LSQ CYCLES= 1 STEPS= 20. NCS= NONE. INITIAL b-FACTOR CORRECTION: NONE. BULK SOLVENT: FALSE. THEORETICAL TOTAL NUMBER OF REFL. IN RESOL. RANGE: 4733 (100.0 % ). NUMBER OF UNOBSERVED REFLECTIONS (NO ENTRY OR |F|=0): 937 (19.8 % ). NUMBER OF REFLECTIONS REJECTED: 664 (14.0 % ). TOTAL NUMBER OF REFLECTIONS USED: 3132 (66.2 % ). NUMBER OF REFLECTIONS IN WORKING SET: 2790 (58.9 % ). NUMBER OF REFLECTIONS IN TEST SET: 342 (7.2 % ).
RfactorNum. reflection% reflection
Rfree0.432 342 -
Rwork0.401 --
obs-2790 66 %
Refinement stepCycle: LAST / Resolution: 7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17660 0 0 0 17660
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 7 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.401
Solvent computation
*PLUS
Displacement parameters
*PLUS

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