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- PDB-1hqy: Nucleotide-Dependent Conformational Changes in a Protease-Associa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hqy | ||||||
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Title | Nucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU | ||||||
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![]() | CHAPERONE / HSLVU / PEPTIDASE-ATPASE COMPLEX | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Wang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() Title: ATP-dependent proteases: Docking of Components in a Bacterial Complex Authors: Ishikawa, T. / Maurizi, M.R. / Belnap, D. / Steven, A.C. #6: ![]() Title: A corrected quaternary arrangement of the peptidase hslv and atpase hslu in a cocrystal structure Authors: Wang, J. | ||||||
History |
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Remark 600 | HETEROGEN ADP 450 IS ASSOCIATED WITH CHAIN E. ADP 1450 IS ASSOCIATED WITH CHAIN F. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.3 KB | Display | ![]() |
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PDB format | ![]() | 243.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 543.2 KB | Display | ![]() |
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Full document | ![]() | 631 KB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 60.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Dodecameric HslV complexed with hexameric HslU |
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Components
#1: Protein | Mass: 18986.641 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 50495.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.14 % |
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Crystal grow | Method: see 1e94 / Details: SEE 1E94 |
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 66.1 Å2 |
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Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 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.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.13 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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