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- PDB-1kyi: HslUV (H. influenzae)-NLVS Vinyl Sulfone Inhibitor Complex -

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Basic information

Entry
Database: PDB / ID: 1kyi
TitleHslUV (H. influenzae)-NLVS Vinyl Sulfone Inhibitor Complex
Components
  • ATP-dependent hsl protease ATP-binding subunit hslU
  • ATP-dependent protease hslV
KeywordsCHAPERONE/HYDROLASE / prokaryotic proteasome / protease / AAA-protein / ATP-dependent chaperone / Clp/Hsp100 / vinyl sulfone inhibitor / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / Chem-LVS / 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: 3.1 Å
AuthorsSousa, M.C. / Kessler, B.M. / Overkleeft, H.S. / McKay, D.B.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of HslUV Complexed with a Vinyl Sulfone Inhibitor: Corroboration of a Proposed Mechanism of Allosteric Activation of HslV by HslU
Authors: Sousa, M.C. / Kessler, B.M. / Overkleeft, H.S. / McKay, D.B.
#1: Journal: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site
Authors: Sousa, M.C. / McKay, D.B.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning
Authors: Trame, C.B. / McKay, D.B.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN ATP 450 IS ASSOCIATED WITH CHAIN A. ATP 451 IS ASSOCIATED WITH CHAIN B. ATP 452 IS ...HETEROGEN ATP 450 IS ASSOCIATED WITH CHAIN A. ATP 451 IS ASSOCIATED WITH CHAIN B. ATP 452 IS ASSOCIATED WITH CHAIN C. ATP 453 IS ASSOCIATED WITH CHAIN D. ATP 454 IS ASSOCIATED WITH CHAIN E. ATP 455 IS ASSOCIATED WITH CHAIN F. ATP 456 IS ASSOCIATED WITH CHAIN S. ATP 457 IS ASSOCIATED WITH CHAIN T. ATP 458 IS ASSOCIATED WITH CHAIN U. ATP 459 IS ASSOCIATED WITH CHAIN V. ATP 460 IS ASSOCIATED WITH CHAIN W. ATP 461 IS ASSOCIATED WITH CHAIN X.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent hsl protease ATP-binding subunit hslU
B: ATP-dependent hsl protease ATP-binding subunit hslU
C: ATP-dependent hsl protease ATP-binding subunit hslU
D: ATP-dependent hsl protease ATP-binding subunit hslU
E: ATP-dependent hsl protease ATP-binding subunit hslU
F: ATP-dependent hsl 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 hsl protease ATP-binding subunit hslU
T: ATP-dependent hsl protease ATP-binding subunit hslU
U: ATP-dependent hsl protease ATP-binding subunit hslU
V: ATP-dependent hsl protease ATP-binding subunit hslU
W: ATP-dependent hsl protease ATP-binding subunit hslU
X: ATP-dependent hsl protease ATP-binding subunit hslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)834,89848
Polymers820,14124
Non-polymers14,75824
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area104440 Å2
ΔGint-323 kcal/mol
Surface area223760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.51, 219.97, 242.63
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
ATP-dependent hsl 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) / Strain: Rd KW20 / Gene: hslU / Plasmid: pET / 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) / Strain: Rd KW20 / Gene: hslV / Plasmid: pET / 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
#4: Chemical
ChemComp-LVS / 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE


Mass: 722.632 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C28H43IN4O8S
Has protein modificationY

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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: 63.73 %
Crystal growTemperature: 277 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 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Details: Sousa, M.C., (2000) Cell (Cambridge,Mass.), 103, 633.
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: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2001
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 185090 / Num. obs: 185090 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.064 / Net I/σ(I): 16.1
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.285 / % possible all: 87.8
Reflection
*PLUS
Num. measured all: 675855 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 87.8 % / Rmerge(I) obs: 0.285

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G3I

1g3i


Resolution: 3.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 6885 -RANDOM
Rwork0.266 ---
all-171914 --
obs-171914 92.9 %-
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45048 0 708 0 45756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.46
LS refinement shellHighest resolution: 3.1 Å
RfactorNum. reflection% reflection
Rfree0.288 6885 -
Rwork0.266 --
obs-171914 0.929 %
Refinement
*PLUS
Rfactor obs: 0.266 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.266 / Rfactor obs: 0.266

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