[English] 日本語
Yorodumi
- PDB-4i4l: Crystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i4l
TitleCrystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer
ComponentsATP-dependent Clp protease ATP-binding subunit ClpX
KeywordsMOTOR PROTEIN / hexamer / wild-type / asymmetric / nucleotide-bound
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding ...protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding / protein dimerization activity / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Clp protease, ATP-binding subunit ClpX, bacteria / Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) ...Clp protease, ATP-binding subunit ClpX, bacteria / Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / 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 / Helicase, Ruva Protein; domain 3 / 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 / ATP-dependent Clp protease ATP-binding subunit ClpX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6981 Å
AuthorsGlynn, S.E. / Nager, A.R. / Stinson, B.S. / Schmitz, K.R. / Baker, T.A. / Sauer, R.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA+ Machine.
Authors: Stinson, B.M. / Nager, A.R. / Glynn, S.E. / Schmitz, K.R. / Baker, T.A. / Sauer, R.T.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
C: ATP-dependent Clp protease ATP-binding subunit ClpX
D: ATP-dependent Clp protease ATP-binding subunit ClpX
E: ATP-dependent Clp protease ATP-binding subunit ClpX
F: ATP-dependent Clp protease ATP-binding subunit ClpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,61813
Polymers236,6156
Non-polymers1,0047
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-191 kcal/mol
Surface area77810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.942, 181.903, 201.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (backbone or name CB) and (resid 67:97...
21chain B and (backbone or name CB) and (resid 67:97...
31chain C and (backbone or name CB) and (resid 67:97...
41chain D and (backbone or name CB) and (resid 67:97...
51chain E and (backbone or name CB) and (resid 67:97...
61chain F and (backbone or name CB) and (resid 67:97...
12chain A and (backbone or name CB) and (resid 319:412)
22chain B and (backbone or name CB) and (resid 319:412)
32chain C and (backbone or name CB) and (resid 319:412)
42chain D and (backbone or name CB) and (resid 319:412)
52chain E and (backbone or name CB) and (resid 319:412)
62chain F and (backbone or name CB) and (resid 319:412)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (backbone or name CB) and (resid 67:97...A63 - 413
121chain A and (backbone or name CB) and (resid 67:97...A63 - 413
211chain B and (backbone or name CB) and (resid 67:97...B63 - 413
221chain B and (backbone or name CB) and (resid 67:97...B63 - 413
311chain C and (backbone or name CB) and (resid 67:97...C63 - 413
321chain C and (backbone or name CB) and (resid 67:97...C63 - 413
411chain D and (backbone or name CB) and (resid 67:97...D63 - 413
421chain D and (backbone or name CB) and (resid 67:97...D63 - 413
511chain E and (backbone or name CB) and (resid 67:97...E63 - 413
521chain E and (backbone or name CB) and (resid 67:97...E63 - 413
611chain F and (backbone or name CB) and (resid 67:97...F63 - 413
621chain F and (backbone or name CB) and (resid 67:97...F63 - 413
112chain A and (backbone or name CB) and (resid 319:412)A0
212chain B and (backbone or name CB) and (resid 319:412)B0
312chain C and (backbone or name CB) and (resid 319:412)C0
412chain D and (backbone or name CB) and (resid 319:412)D0
512chain E and (backbone or name CB) and (resid 319:412)E0
612chain F and (backbone or name CB) and (resid 319:412)F0

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.624283, 0.691705, 0.363064), (-0.743743, 0.384082, 0.547108), (0.238991, -0.611576, 0.754227)39.561298, 22.5156, -14.8208
2given(0.147847, 0.484668, 0.862112), (-0.630522, -0.625384, 0.459714), (0.76196, -0.611548, 0.213133)68.348503, 1.68583, -38.103298
3given(0.630884, -0.655441, 0.41519), (-0.582207, -0.753638, -0.305066), (0.512856, -0.049265, -0.85706)7.13153, -21.0375, -69.477997
4given(-0.122464, -0.979217, -0.161665), (-0.379664, 0.196724, -0.903966), (0.916983, -0.049325, -0.395865)21.937201, -31.5993, -54.330799
5given(0.193832, -0.662336, -0.723699), (0.358703, 0.734458, -0.57611), (0.913105, -0.147925, 0.379943)6.03775, -34.139599, -31.163
6given(0.745528, 0.63338, 0.207407), (-0.577704, 0.458961, 0.674991), (0.332334, -0.623044, 0.708075)25.1187, 27.430599, -21.340599
7given(0.947725, 0.229153, 0.222049), (-0.005581, -0.683876, 0.729577), (0.319039, -0.692678, -0.646847)-6.36112, -6.10718, -76.491798
8given(0.40517, -0.785339, 0.46806), (-0.818363, -0.539782, -0.197275), (0.407579, -0.303113, -0.861396)22.2691, -7.88687, -63.2104
9given(0.03237, -0.990434, 0.13414), (-0.23972, -0.137986, -0.960986), (0.970302, -0.001049, -0.241893)16.6891, -35.186901, -55.977299
10given(0.510868, -0.798015, 0.319666), (0.786712, 0.284089, -0.548068), (0.346553, 0.531475, 0.772939)-7.20925, -47.18, -16.23

-
Components

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpX


Mass: 39435.793 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0438, clpX, JW0428, lopC / Plasmid: pACYC / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P0A6H1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.8
Details: 75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.698→50 Å / Num. all: 21372 / Num. obs: 21372 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Χ2: 1.023 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.698-3.833.40.30920980.56195.3
3.83-3.993.80.26921310.754194.9
3.99-4.173.90.19421370.768196.9
4.17-4.393.90.16521091.037193.5
4.39-4.6640.11821480.926194.6
4.66-5.023.90.10121460.955195.5
5.02-5.5340.121270.905194
5.53-6.3240.08821220.902192.5
6.32-7.963.90.06421501.423192
7.96-503.60.03722041.976189.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HWS

3hws


Resolution: 3.6981→45.476 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7302 / SU ML: 0.59 / σ(F): 0.11 / Phase error: 32.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3227 1026 5.02 %RANDOM
Rwork0.2997 ---
all0.3009 20446 --
obs0.3009 20446 89.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.102 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 475.11 Å2 / Biso mean: 145.9978 Å2 / Biso min: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.8875 Å20 Å2-0 Å2
2--4.54 Å20 Å2
3----0.6525 Å2
Refinement stepCycle: LAST / Resolution: 3.6981→45.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13647 0 57 0 13704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213842
X-RAY DIFFRACTIONf_angle_d0.43918745
X-RAY DIFFRACTIONf_chiral_restr0.0282291
X-RAY DIFFRACTIONf_plane_restr0.0022393
X-RAY DIFFRACTIONf_dihedral_angle_d9.9395009
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A655X-RAY DIFFRACTIONPOSITIONAL0.009
12B655X-RAY DIFFRACTIONPOSITIONAL0.009
13C655X-RAY DIFFRACTIONPOSITIONAL0.01
14D655X-RAY DIFFRACTIONPOSITIONAL0.008
15E511X-RAY DIFFRACTIONPOSITIONAL0.01
16F655X-RAY DIFFRACTIONPOSITIONAL0.01
21A466X-RAY DIFFRACTIONPOSITIONAL0.113
22B466X-RAY DIFFRACTIONPOSITIONAL0.113
23C466X-RAY DIFFRACTIONPOSITIONAL0.138
24D466X-RAY DIFFRACTIONPOSITIONAL0.107
25E466X-RAY DIFFRACTIONPOSITIONAL0.134
26F466X-RAY DIFFRACTIONPOSITIONAL0.139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6981-3.8930.36091270.35632507263483
3.893-4.13680.38421500.3332698284889
4.1368-4.45590.32071450.30712754289990
4.4559-4.90390.33761480.2952809295792
4.9039-5.61230.33261650.32022826299191
5.6123-7.06670.35311300.32862869299991
7.0667-45.47920.2551610.24112957311890

+
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