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- PDB-5ji3: HslUV complex -

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Basic information

Entry
Database: PDB / ID: 5ji3
TitleHslUV complex
Components
  • ATP-dependent protease ATPase subunit HslU
  • ATP-dependent protease subunit HslV
KeywordsHYDROLASE / AAA+ ATPase / peptidase / HSLVU / PEPTIDASE-ATPASE COMPLEX / 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 / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / 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 ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / 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 subunit HslV / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGrant, R.A. / Sauer, R.T. / Schmitz, K.R. / Baytshtok, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health5R01AI016892-36 United States
National Institutes of Health5R01GM1011988-37 United States
Citation
Journal: Structure / Year: 2016
Title: A Structurally Dynamic Region of the HslU Intermediate Domain Controls Protein Degradation and ATP Hydrolysis.
Authors: Baytshtok, V. / Fei, X. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
#1: 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.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,6138
Polymers175,7916
Non-polymers8222
Water00
1
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules

A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules

A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)529,83924
Polymers527,37218
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
MethodPISA
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
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and ((resid 1 and (name N or name...
211(chain B and ((resid 1 and (name N or name...
311(chain C and ((resid 1 and (name N or name...
411(chain D and ((resid 1 and (name N or name...

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Components

#1: Protein
ATP-dependent protease subunit HslV / Heat shock protein HslV


Mass: 19117.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hslV, EC55989_4410 / Production host: Escherichia coli (E. coli)
References: UniProt: B7LA29, UniProt: P0A7B8*PLUS, HslU-HslV peptidase
#2: Protein ATP-dependent protease ATPase subunit HslU / Heat shock protein HslU / Unfoldase HslU


Mass: 49659.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hslU, htpI, Z5478, ECs4858 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H6, UniProt: P0A6H5*PLUS
#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: 4.28 Å3/Da / Density % sol: 71.24 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: NA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection% possible obs: 85.7 % / Redundancy: 2 % / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
CNS(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
PHENIX(1.10_2155: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4A

1g4a


Resolution: 3→84.997 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 39.89
Details: data were downloaded as mmCIF file from PDB 1G4A and converted to MTZ format for re-refinement of the model
RfactorNum. reflection% reflection
Rfree0.2525 4864 10.45 %
Rwork0.2217 --
obs0.2287 46550 85.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→84.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10975 0 52 0 11027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211163
X-RAY DIFFRACTIONf_angle_d0.49415082
X-RAY DIFFRACTIONf_dihedral_angle_d15.0816830
X-RAY DIFFRACTIONf_chiral_restr0.0421775
X-RAY DIFFRACTIONf_plane_restr0.0031950
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A696X-RAY DIFFRACTIONPOSITIONAL
12B696X-RAY DIFFRACTIONPOSITIONAL0.02
13C696X-RAY DIFFRACTIONPOSITIONAL0.03
14D696X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.05270.36992170.33191819X-RAY DIFFRACTION69
3.0527-3.10820.3332670.31651927X-RAY DIFFRACTION71
3.1082-3.1680.36972260.29822011X-RAY DIFFRACTION74
3.168-3.23260.32462350.29892018X-RAY DIFFRACTION76
3.2326-3.30290.32672430.29692070X-RAY DIFFRACTION77
3.3029-3.37970.32722360.27342020X-RAY DIFFRACTION76
3.3797-3.46420.27562280.27192148X-RAY DIFFRACTION79
3.4642-3.55780.2762220.26012085X-RAY DIFFRACTION78
3.5578-3.66250.3082370.26272146X-RAY DIFFRACTION79
3.6625-3.78060.24992090.24942153X-RAY DIFFRACTION80
3.7806-3.91570.27922150.242174X-RAY DIFFRACTION81
3.9157-4.07240.29012320.22552089X-RAY DIFFRACTION78
4.0724-4.25760.2682470.21282189X-RAY DIFFRACTION80
4.2576-4.48190.252560.19352102X-RAY DIFFRACTION78
4.4819-4.76250.19932520.17842138X-RAY DIFFRACTION79
4.7625-5.12980.20122050.17992179X-RAY DIFFRACTION80
5.1298-5.64520.21052380.20442133X-RAY DIFFRACTION78
5.6452-6.46030.24182170.21442154X-RAY DIFFRACTION78
6.4603-8.13240.20982320.1932148X-RAY DIFFRACTION77
8.1324-46.95480.20992330.19682165X-RAY DIFFRACTION75

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