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- PDB-1hqy: Nucleotide-Dependent Conformational Changes in a Protease-Associa... -

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Basic information

Entry
Database: PDB / ID: 1hqy
TitleNucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU
Components
  • HEAT SHOCK LOCUS HSLU
  • HEAT SHOCK LOCUS HSLV
KeywordsCHAPERONE / HSLVU / PEPTIDASE-ATPASE 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 / cellular response to heat / peptidase activity ...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 / cellular response to heat / peptidase activity / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / membrane / identical protein binding / cytosol
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 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV / ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsWang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H.
Citation
Journal: Structure / Year: 2001
Title: Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU.
Authors: Wang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Mutational Studies of Hslu and its Docking Mode With Hslv.
Authors: Song, H.K. / Hartmann, C. / Ramachandran, R. / Bochtler, M. / Behrendt, R. / Moroder, L. / Huber, R.
#2: Journal: Nature / Year: 2000
Title: The Structures 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.
#3: 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, S. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B.
#4: 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.
#5: Journal: Nature / Year: 2000
Title: ATP-dependent proteases: Docking of Components in a Bacterial Complex
Authors: Ishikawa, T. / Maurizi, M.R. / Belnap, D. / Steven, A.C.
#6: Journal: J.STRUCT.BIOL. / Year: 2001
Title: A corrected quaternary arrangement of the peptidase hslv and atpase hslu in a cocrystal structure
Authors: Wang, J.
History
DepositionDec 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 25, 2013Group: Derived calculations
Revision 1.4May 30, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN ADP 450 IS ASSOCIATED WITH CHAIN E. ADP 1450 IS ASSOCIATED WITH CHAIN F.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,7928
Polymers176,9386
Non-polymers8542
Water0
1
A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
hetero molecules

A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
hetero molecules

A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,45618
Polymers416,89312
Non-polymers2,5636
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
2
C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV

C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV

C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV


Theoretical massNumber of molelcules
Total (without water)113,9206
Polymers113,9206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Unit cell
Length a, b, c (Å)172.022, 172.022, 276.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsDodecameric HslV complexed with hexameric HslU

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Components

#1: Protein
HEAT SHOCK LOCUS HSLV / ATP-DEPENDENT PROTEASE HSLV


Mass: 18986.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P31059, UniProt: P0A7B8*PLUS
#2: Protein HEAT SHOCK LOCUS HSLU / ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU


Mass: 50495.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6H5
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growMethod: see 1e94 / Details: SEE 1E94

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 66.1 Å2

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementResolution: 2.8→29.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 683901.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THIS ENTRY CONTAINS A PSEUDO-SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS AUTHOR BELIEVES THIS ENTRY, ...Details: THIS ENTRY CONTAINS A PSEUDO-SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS AUTHOR BELIEVES THIS ENTRY, WHICH HAS BEEN REVISED FROM THE ENTRY 1E94, IS A PSEUDO-SOLUTION, BECAUSE THE SPACE GROUP WAS INCORRECT ASSIGNED AND X-RAY DIFFRACTION DATA WERE INCORRECTLY AVERAGED AND PROCESSED IN 1E94. THE ASSIGNMENT OF THE SCREW AXIS 6(3) IN THE P6(3)22 SPACE GROUP FOR THE HSLVU COMPLEX STRUCTURES DESCRIBED IN REFERENCES 1 AND 2 BELOW (CORRESPONDING PDB ACCESSION NUMBERS ARE 1DOO AND 1E94, RESPECTIVELY) REQUIRES THE PRESENCE OF SYSTEMATIC EXTINCTIONS ALONG (00L) WITH L=2N+1. THERE WERE NO SYSTEMATIC EXTINCTIONS AT ALL IN THE 1E94SF ENTRY. THERE WERE TWO REFLECTIONS WITH F/SIGMA(F) NEAR 20 AND NINE REFLECTIONS WITH F/SIMGA(F) OVER 10 ALONG (00L) WITH L=2N+1. SUCH A LARGE NUMBER OF SIGNIFICANT OBSERVATIONS CANNOT BE DUE TO TECHNICAL ERRORS IN MEASUREMENT OF X-RAY DIFFRACTION DATA. A STATISTICAL ANALYSIS OF THEM COMPARED WITH THE REST OF THE DATA CONFIRMS THAT THEY ARE NOT DUE TO TECHNICAL ERRORS. THEREFORE, THE SPACE GROUP MUST NOT BE P6(3)22. LARGE VALUES OF COMBINED R-MERGE VALUES FOR OBSERVED DATA 1DOO (14.1%) AND 1E94 (12.1%) ARE INDICATIVE OF INCORRECT ASSIGNEMENT OF POINT SYMMETRY GROUP TO BE 622. THE ESTIMATED MEASUREMENT PRECISION IN INTENSITY SHOULD BE ABOUT 1% ON THE BASIS OF THE AVERAGE F/SIGMA(F) OF 44.7 IN 1E94 OBSERVED DATA. THEREFORE, ONE SETS OF DYADS IN THE POINT SYMMETRY P622 WERE TWINNING OPERATIONS. THERE WERE LARGE DISCREPANCIES IN WILSON RATIO (/^2) BETWEEN THE OBSERVED DATA AND CALCULATED DATA FROM THE COORDINATE 1E94 IN THE FOLLOWING ZONES: L=2N, L=2N+1, H+K=3N/L=2N; H+K != 3N/L=2N, AND ALL HKL. SOME WERE LARGE THAN 70% AND SOME WERE AS SMALL AS 5%. THIS SUGGESTS THAT X-RAY DATA WERE PROCESSED FROM TWINNED CRYSTALS. THERE WERE ALSO LARGE DIFFERENCES IN THE FIRST AND SECOND MOMENTS OF THE DIFFERENCES (FOBS-FCALC). THIS IS ANOTHER STATISTICAL INDICATOR FOR THE TWINNING PROBLEM. BECAUSE OF THE SEVERE ERRORS IN SPACE GROUP ASSIGNMENT AND DATA PROCESSING, ANY STRUCTURAL SOLUTIONS ARE PSEUDO-SOLUTIONS, WHICH FIT ONLY A PORTION OF THE ORIGINAL OBSERVATIONS. DESPITE OF THESE SEVERE ERRORS, USING THE OBSERVED 1E94 DATA, THIS AUTHOR WAS ABLE TO SHOW TWO ADDITIONAL RESULTS IN THE PSEUDO-SOLUTION TO THE X-RAY DATA OF 1E94SF DIFFERENT FROM THE ORIGINAL AUTHORS. (1). THE BOUND NUCLEOTIDE WAS ADP IN AN ANTI CONFORMATION, NOT AS THE ORIGINAL AUTHORS CLAIMED THAT THE NUCLEOTIDE WAS AMPPNP IN A SYN CONFORMATION. THIS FINDING AGREES WITH REFERENCES 3 AND 4 IN NUCLEOTIDE CONFORMATION AND HSLU CONFORMATION. (2). THE BIOLOGICALLY RELEVANT HSLVU COMPLEX WAS CLEARLY PRESENT IN THE X-RAY DIFFRACTION DATA, IN WHICH HSLU SUBUNITS E AND F WERE TRANSLATED BY 158 ANGSTRONMS IN ASYMMETRIC UNIT. THIS COMPLEX CONTRIBUTED ABOUT 8% OF THE OBSERVED 1E94 INTENSITY DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.333 5612 10.1 %RANDOM
Rwork0.287 ---
obs0.287 55365 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.13 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 70.2 Å2
Baniso -1Baniso -2Baniso -3
1--11.93 Å26.12 Å20 Å2
2---11.93 Å20 Å2
3---23.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11764 0 54 0 11818
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.32.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.464 823 10.1 %
Rwork0.4 7308 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP.PARADP.TOP

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