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- PDB-1g3i: CRYSTAL STRUCTURE OF THE HSLUV PROTEASE-CHAPERONE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1g3i
TitleCRYSTAL STRUCTURE OF THE HSLUV PROTEASE-CHAPERONE COMPLEX
Components
  • ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
  • ATP-DEPENDENT PROTEASE HSLV
KeywordsCHAPERONE/HYDROLASE / CHAPERONE-HYDROLASE complex
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding ...HslU-HslV peptidase / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding / 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 / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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 / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent protease subunit HslV / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsSousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal and solution structures of an HslUV protease-chaperone complex.
Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
C: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
D: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
E: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
G: ATP-DEPENDENT PROTEASE HSLV
H: ATP-DEPENDENT PROTEASE HSLV
I: ATP-DEPENDENT PROTEASE HSLV
J: ATP-DEPENDENT PROTEASE HSLV
K: ATP-DEPENDENT PROTEASE HSLV
L: ATP-DEPENDENT PROTEASE HSLV
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV
Q: ATP-DEPENDENT PROTEASE HSLV
R: ATP-DEPENDENT PROTEASE HSLV
S: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
T: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
U: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
V: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
W: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
X: ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)826,22736
Polymers820,14124
Non-polymers6,08612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area92590 Å2
ΔGint-248 kcal/mol
Surface area232070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.223, 220.579, 241.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the complex HslU12-HslV12 seen in the asymmetric unit.

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Components

#1: Protein
ATP-DEPENDENT HSLU PROTEASE ATP-BINDING SUBUNIT HSLU / HSLU


Mass: 49441.504 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43773
#2: Protein
ATP-DEPENDENT PROTEASE HSLV / HSLV


Mass: 18903.549 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43772, EC: 3.4.99.-
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG monomethyl ether 2000, potassium Chloride, magnesium acetate, citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-20 mg/mlprotein1drop
210 mMMOPS1drop
31 mM1dropMg(OAc)2
41 mMATP1drop
53-6 %PEG2000MME1reservoir
61 M1reservoirKCl
710 mM1reservoirMg(OAc)2
850 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. all: 134912 / Num. obs: 134912 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.5
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3 / % possible all: 80.6
Reflection
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 30 Å / Num. measured all: 297864
Reflection shell
*PLUS
Highest resolution: 3.4 Å / % possible obs: 80.6 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: H. influenzae HslU at 2.3A H. influenzae HslV at 1.9A

Resolution: 3.41→30.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 9712778.95 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 6383 5 %RANDOM
Rwork0.24 ---
obs0.24 126814 --
all-134912 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.96 Å2 / ksol: 0.238 e/Å3
Displacement parametersBiso mean: 102.9 Å2
Baniso -1Baniso -2Baniso -3
1--28.95 Å20 Å20 Å2
2---7.75 Å20 Å2
3---36.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 3.41→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45156 0 372 0 45528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 852 5.1 %
Rwork0.344 15794 -
obs--65.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BILL_DNA-RNA-ATP_REP.PARAMBILL_ATP.TOP2
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 102.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.344

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