[English] 日本語
Yorodumi
- PDB-1ksf: Crystal Structure of ClpA, an HSP100 chaperone and regulator of C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ksf
TitleCrystal Structure of ClpA, an HSP100 chaperone and regulator of ClpAP protease: Structural basis of differences in Function of the Two AAA+ ATPase domains
ComponentsATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
KeywordsHYDROLASE / LIGAND BINDING PROTEIN / ClpA / AAA+ / ATPases / ATP-dependent protease / Chaperones
Function / homology
Function and homology information


endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / cellular response to heat / response to oxidative stress / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component ...Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / Helicase, Ruva Protein; domain 3 - #60 / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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 / ISOPROPYL ALCOHOL / METHIONINE / TRIETHYLENE GLYCOL / ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsGuo, F. / Maurizi, M.R. / Esser, L. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of ClpA, an HSP100 chaperone and regulator of ClpAP protease
Authors: Guo, F. / Maurizi, M.R. / Esser, L. / Xia, D.
History
DepositionJan 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,95713
Polymers84,3041
Non-polymers1,65312
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.107, 124.107, 97.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Cell settinghexagonal
Space group name H-MP65

-
Components

-
Protein , 1 types, 1 molecules X

#1: Protein ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA / endopeptidase Clp ATP-binding / ATP-binding component of serine protease


Mass: 84303.812 Da / Num. of mol.: 1 / Mutation: M169I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9

-
Non-polymers , 6 types, 254 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: 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
#6: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: iso-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 294K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 %satammonium sulfate1drop
212 mg/mlprotein1drop
30.1 MHEPES1droppH7.5
410 %glycerol1drop
58 mMATPgammaS1dropor ADP
640 mM1dropMgCl2
70.1 MHEPES1reservoirpH7.5
80.5 M1reservoirKCl
95 %glycerol1reservoir
108 %isopropanol1reservoir
110.01 %sodium azide1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9B11
SYNCHROTRONAPS 5ID-B21
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
MARRESEARCH2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 22312 / % possible obs: 100 %
Reflection shellHighest resolution: 2.6 Å / Rmerge(I) obs: 0.493 / % possible all: 100

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMAC5refinement
CCP4phasing
RefinementResolution: 2.6→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30422 1396 5.9 %RANDOM
Rwork0.21554 ---
obs0.22075 22312 100 %-
Displacement parametersBiso mean: 49.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0.58 Å20 Å2
2---1.15 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5583 0 84 262 5929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.01905762
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.97773
X-RAY DIFFRACTIONr_planar_d
X-RAY DIFFRACTIONr_hb_or_metal_coord
X-RAY DIFFRACTIONr_mcbond_it1.6823556
X-RAY DIFFRACTIONr_mcangle_it3.9465720
X-RAY DIFFRACTIONr_scbond_it6.6042206
X-RAY DIFFRACTIONr_scangle_it8.7882053
X-RAY DIFFRACTIONr_plane_restr
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_singtor_nbd
X-RAY DIFFRACTIONr_multtor_nbd
X-RAY DIFFRACTIONr_xhyhbond_nbd
X-RAY DIFFRACTIONr_xyhbond_nbd
X-RAY DIFFRACTIONr_planar_tor
X-RAY DIFFRACTIONr_staggered_tor
X-RAY DIFFRACTIONr_orthonormal_tor
X-RAY DIFFRACTIONr_transverse_tor
X-RAY DIFFRACTIONr_special_tor
LS refinement shellHighest resolution: 2.6 Å / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.208 / Total num. of bins used: 20
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.3 / Rfactor Rwork: 0.21

+
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