[English] 日本語
Yorodumi
- PDB-1g4b: CRYSTAL STRUCTURES OF THE HSLVU PEPTIDASE-ATPASE COMPLEX REVEAL A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g4b
TitleCRYSTAL STRUCTURES OF THE HSLVU PEPTIDASE-ATPASE COMPLEX REVEAL AN ATP-DEPENDENT PROTEOLYSIS MECHANISM
Components
  • ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
  • ATP-DEPENDENT PROTEASE HSLV
KeywordsCHAPERONE/HYDROLASE / HSLVU / PEPTIDASE-ATPASE COMPLEX / CHAPERONE-HYDROLASE 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 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 7 Å
AuthorsWang, 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.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Purification and Characterization of the Heat Shock Proteins HslV and HslU that form a New ATP-Dependent Protease in Escherichia Coli
Authors: Yoo, S.J. / Seol, J.H. / Shin, D.H. / Rohrwild, M. / Kang, M.S. / Tanaka, K. / Goldberg, A.L. / Chung, C.H.
#2: Journal: Nature / Year: 2000
Title: The Structuers 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.
History
DepositionOct 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV


Theoretical massNumber of molelcules
Total (without water)274,5858
Polymers274,5858
Non-polymers00
Water0
1
E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV

E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV

E: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
F: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
K: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
L: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
O: ATP-DEPENDENT PROTEASE HSLV
P: ATP-DEPENDENT PROTEASE HSLV


Theoretical massNumber of molelcules
Total (without water)823,75624
Polymers823,75624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)173.376, 173.376, 254.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein
ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU / HEAT SHOCK LOCUS HSLU ATPASE


Mass: 49659.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H5
#2: Protein
ATP-DEPENDENT PROTEASE HSLV / HEAT SHOCK LOCUS HSLV PEPTIDASE


Mass: 18986.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7B8, EC: 3.4.99.-

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growMethod: vapor diffusion / Details: dADP-HslU-HslV, VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127 mg/mlprotein1drop
20.1 MMES1reservoir
31.5 M1reservoirNaAc
420 mMTris-HCl1drop
55 mM1dropMgCl2
60.5 mMEDTA1drop
71 mMdithiothreitol1drop
810 %glycerol1drop

-
Data collection

Diffraction sourceSource: ROTATING ANODE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 7 Å / Lowest resolution: 80 Å / Num. obs: 6489 / % possible obs: 87 % / Rmerge(I) obs: 0.201

-
Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 7→10 Å
Details: There are approximately 200 close contacts present within the asymmetric unit and 300 close contacts among crystal symmetry related subunits. These contacts resulted from a standard rigid- ...Details: There are approximately 200 close contacts present within the asymmetric unit and 300 close contacts among crystal symmetry related subunits. These contacts resulted from a standard rigid-body refinement during which contact penalty was not included. These contacts may imply domain motions with each subunit, which is yet to be resolved at higher resolutions. RIGID-BODY REFINEMENT ONLY WITH ONE BODY PER SUBUNIT. COORDINATES FROM TWINNED DATA RIGID-BODY REFINEMENT. TWINNING OPERATOR= -H,-K,L TWINNING FRACTION= .500. REFINEMENT RESOLUTION: 10 - 7 A. STARTING TWINNED R= 0.4447 TWINNED FREE_R= 0.4607. FINAL TWINNED R= 0.4008 TWINNED FREE_R= 0.4322. TARGET= TWIN_LSQ CYCLES= 1 STEPS= 20. NCS= NONE. INITIAL b-FACTOR CORRECTION: NONE. BULK SOLVENT: FALSE. THEORETICAL TOTAL NUMBER OF REFL. IN RESOL. RANGE: 4733 (100.0 % ). NUMBER OF UNOBSERVED REFLECTIONS (NO ENTRY OR |F|=0): 937 (19.8 % ). NUMBER OF REFLECTIONS REJECTED: 664 (14.0 % ). TOTAL NUMBER OF REFLECTIONS USED: 3132 (66.2 % ). NUMBER OF REFLECTIONS IN WORKING SET: 2790 (58.9 % ). NUMBER OF REFLECTIONS IN TEST SET: 342 (7.2 % ).
RfactorNum. reflection% reflection
Rfree0.432 342 -
Rwork0.401 --
obs-2790 66 %
Refinement stepCycle: LAST / Resolution: 7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17660 0 0 0 17660
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 7 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.401
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more