[English] 日本語
Yorodumi
- EMDB-20412: ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20412
TitleClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2
Map data
Sample
  • Complex: ClpX-ClpP-substrate-ATPrS
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: substrate peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsProtein degradation / AAA+ protease complex / CHAPERONE
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / proteasomal protein catabolic process ...protein denaturation / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / disordered domain specific binding / unfolded protein binding / protein folding / peptidase activity / ATPase binding / response to heat / protease binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / : / ClpP, Ser active site / Endopeptidase Clp serine active site. ...Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / : / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ClpP/crotonase-like domain superfamily / 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 Clp protease ATP-binding subunit ClpX / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit ClpX / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsFei X / Jenni S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-101988 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2020
Title: Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.
Authors: Xue Fei / Tristan A Bell / Simon Jenni / Benjamin M Stinson / Tania A Baker / Stephen C Harrison / Robert T Sauer /
Abstract: ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the ...ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.
History
DepositionJul 3, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseMar 11, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6pod
  • Surface level: 3.01
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6pod
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20412.png

Downloads & links

-
Map

FileDownload / File: emd_20412.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.16 Å/pix.
x 192 pix.
= 222.72 Å		1.16 Å/pix.
x 192 pix.
= 222.72 Å		1.16 Å/pix.
x 192 pix.
= 222.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.01 / Movie #1: 3.01
Minimum - Maximum-11.270491 - 21.958594999999999
Average (Standard dev.)-0.00000000000368 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z222.720222.720222.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-11.27021.959-0.000

-
Supplemental data

-
Sample components

-
Entire : ClpX-ClpP-substrate-ATPrS

EntireName: ClpX-ClpP-substrate-ATPrS
Components
  • Complex: ClpX-ClpP-substrate-ATPrS
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: substrate peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: ClpX-ClpP-substrate-ATPrS

SupramoleculeName: ClpX-ClpP-substrate-ATPrS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpX / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 39.835129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SALPTPHEIR NHLDDYVIGQ EQAKKVLAVA VYNHYKRLRN GDTSNGVELG KSNILLIGPT GSGKTLLAET LARLLDVPFT MADATTLTE AGYVGEDVEN IIQKLLQKSD YDVQKAQRGI VYIDQIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA A VPPQGGRK ...String:
SALPTPHEIR NHLDDYVIGQ EQAKKVLAVA VYNHYKRLRN GDTSNGVELG KSNILLIGPT GSGKTLLAET LARLLDVPFT MADATTLTE AGYVGEDVEN IIQKLLQKSD YDVQKAQRGI VYIDQIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA A VPPQGGRK HPQQEFLQVD TSKILFICGG AFAGLDKVIS HRVETGSGIG FGATVKAKSD KASEGELLAQ VEPEDLIKFG LI PEFIGRL PVVATLNELS EEALIQILKE PKNALTKQYQ ALFNLEGVDL EFRDEALDAI AKKAMARKTG ARGLRSIVEA ALL DTMYDL PSMEDVEKVV IDESVIDGQS EPLLIYGKPE AQQASGEGGG TSG

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpX

-
Macromolecule #2: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.21265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYSGERDNF APHMALVPMV IEQTSRGERS FDIYSRLLKE RVIFLTGQVE DHMANLIVAQ MLFLEAENPE KDIYLYINSP GGVITAGMS IYDTMQFIKP DVSTICMGQA ASMGAFLLTA GAKGKRFCLP NSRVMIHQPL GGYQGQATDI EIHAREILKV K GRMNELMA ...String:
MSYSGERDNF APHMALVPMV IEQTSRGERS FDIYSRLLKE RVIFLTGQVE DHMANLIVAQ MLFLEAENPE KDIYLYINSP GGVITAGMS IYDTMQFIKP DVSTICMGQA ASMGAFLLTA GAKGKRFCLP NSRVMIHQPL GGYQGQATDI EIHAREILKV K GRMNELMA LHTGQSLEQI ERDTERDRFL SAPEAVEYGL VDSILTHRN

UniProtKB: ATP-dependent Clp protease proteolytic subunit

-
Macromolecule #3: substrate peptide

MacromoleculeName: substrate peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.635006 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

-
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Average exposure time: 60.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: -2.5 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus min: -0.8 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Details2X binned and motioncor2 corrected
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3mt6

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 241899
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

3hws

chain_id: A, source_name: PDB, initial_model_type: experimental model

3mt6

source_name: PDB, initial_model_type: experimental model
Output model

PDB-6pod:
ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2

+
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