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- PDB-1ht1: Nucleotide-Dependent Conformational Changes in a Protease-Associa... -

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Basic information

Entry
Database: PDB / ID: 1ht1
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 / protein unfolding / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / cellular response to heat / response to heat ...HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / cellular response to heat / response to heat / peptidase activity / protein domain specific binding / ATP hydrolysis activity / proteolysis / magnesium ion binding / membrane / ATP binding / 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 / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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 / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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 / Nucleophile aminohydrolases, N-terminal / Helicase, Ruva Protein; domain 3 / 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
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 27, 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 1.4Aug 10, 2016Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV
V: HEAT SHOCK LOCUS HSLV
X: HEAT SHOCK LOCUS HSLV
A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
Z: HEAT SHOCK LOCUS HSLV
Y: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
G: HEAT SHOCK LOCUS HSLU
I: HEAT SHOCK LOCUS HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,58416
Polymers353,87512
Non-polymers1,7094
Water0
1
A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
Z: HEAT SHOCK LOCUS HSLV
Y: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
G: HEAT SHOCK LOCUS HSLU
I: HEAT SHOCK LOCUS HSLU
hetero molecules

A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
Z: HEAT SHOCK LOCUS HSLV
Y: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
G: HEAT SHOCK LOCUS HSLU
I: HEAT SHOCK LOCUS HSLU
hetero molecules

A: HEAT SHOCK LOCUS HSLV
B: HEAT SHOCK LOCUS HSLV
Z: HEAT SHOCK LOCUS HSLV
Y: HEAT SHOCK LOCUS HSLV
E: HEAT SHOCK LOCUS HSLU
F: HEAT SHOCK LOCUS HSLU
G: HEAT SHOCK LOCUS HSLU
I: HEAT SHOCK LOCUS HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)838,91236
Polymers833,78624
Non-polymers5,12612
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
V: HEAT SHOCK LOCUS HSLV
X: HEAT SHOCK LOCUS HSLV

C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV
V: HEAT SHOCK LOCUS HSLV
X: HEAT SHOCK LOCUS HSLV

C: HEAT SHOCK LOCUS HSLV
D: HEAT SHOCK LOCUS HSLV
V: HEAT SHOCK LOCUS HSLV
X: HEAT SHOCK LOCUS HSLV


Theoretical massNumber of molelcules
Total (without water)227,84012
Polymers227,84012
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 number150
Space group name H-MP321

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Components

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


Mass: 18986.641 Da / Num. of mol.: 8
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: P0A7B8
#2: Protein
HEAT SHOCK LOCUS HSLU / ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU


Mass: 50495.531 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: P0A6H5
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / 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 grow
*PLUS
Method: unknown

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Data collection

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

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementResolution: 2.8→29.62 Å / Data cutoff high absF: 683901.76 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THIS ENTRY CONTAINS A SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS ENTRY IS RELATED TO 1HQY, 1HT2 AND ...Details: THIS ENTRY CONTAINS A SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS ENTRY IS RELATED TO 1HQY, 1HT2 AND 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 (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. THE CORRECT POINT GROUP OF 1E94 SHOULD BE LOWER THAN P622, BECAUSE OF LARGE RMERGE VALUES AS INDICATIVE OF NON 50%:50% TWINNING. THE CORRECT SPACE GROUP SHOULD BE EITHER P321 OR P312. THE SPACE GROUP SHOULD ONLY BE DETERMINED FROM THE ORIGINAL INTEGRATED DATA BEFORE SCALING, SO SHOULD BE THE CORRECT TWINNING FRACTION. WITHOUT THE ORIGINAL DATA, THE TWINNING FRACTION COULD ONLY BE TREATED AS 50%:50% AND THE SPACE GROUP SHOULD BE CONSIDERED TO BE EITHER P321 (THIS ENTRY) OR P312 (ENTRY 1HT2). THE DATA TO THE LOWER SPACE GROUP WERE EXPANDED BY THE (-H,-K,L) OPERATION. THE STRUCTURE FACTOR FILE WAS TAKEN FROM 1E94 AND EXPANDED BY THE (-H,-K,L) OPERATION WITH FREE R-FACTOR SELECTION INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1093 9.4 %CHOSEN IN P622 POINT GROUP
Rwork0.261 ---
obs-108031 92.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23528 0 108 0 23636
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP.PARADP.TOP

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