[English] 日本語
Yorodumi
- EMDB-39161: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39161
TitleCryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
Map data
Sample
  • Complex: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
KeywordsMycobacterium tuberculosis / Caseinolytic protease system / Activation / HYDROLASE
Function / homology
Function and homology information


negative regulation of protein polymerization / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone / unfolded protein binding ...negative regulation of protein polymerization / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone / unfolded protein binding / ATPase binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / zinc ion binding / ATP binding / plasma membrane / 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 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsZhou B / Zhao H / Gao Y / Chen X / Zhang T / He J / Xiong X
Funding support China, 9 items
OrganizationGrant numberCountry
Other government2021YFA1300903
Other government2021YFA1300904
National Natural Science Foundation of China (NSFC)32300152 China
National Natural Science Foundation of China (NSFC)81973372 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)32241021 China
National Natural Science Foundation of China (NSFC)82341085 China
Other government2022A1515110505
Other government2022M723164
CitationJournal: To Be Published
Title: Activation mechanism of caseinolytic chaperone-protease system in Mycobacterium tuberculosis by the anti-cancer drug bortezomib
Authors: Zhou B / Zhao H / Gao Y / Chen X / Zhang T / He J / Xiong X
History
DepositionFeb 18, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39161.png

Downloads & links

-
Map

FileDownload / File: emd_39161.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 512 pix.
= 363.52 Å		0.71 Å/pix.
x 512 pix.
= 363.52 Å		0.71 Å/pix.
x 512 pix.
= 363.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.05194734 - 0.67790484
Average (Standard dev.)0.00209629 (±0.014643862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 363.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_39161_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39161_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39161_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bor...

EntireName: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
Components
  • Complex: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE

-
Supramolecule #1: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bor...

SupramoleculeName: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

-
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: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 39.05775 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ELPKPAEIRE FLEGYVIGQD TAKRTLAVAV YNHYKRIQAG EKGRDSRCEP VELTKSNILM LGPTGCGKTY LAQTLAKMLN VPFAIADAT ALTEAGYVGE DVENILLKLI QAADYDVKRA ETGIIYIDQV DKIARKSENP SITRDVSGEG VQQALLKILE G TQASVPPQ ...String:
ELPKPAEIRE FLEGYVIGQD TAKRTLAVAV YNHYKRIQAG EKGRDSRCEP VELTKSNILM LGPTGCGKTY LAQTLAKMLN VPFAIADAT ALTEAGYVGE DVENILLKLI QAADYDVKRA ETGIIYIDQV DKIARKSENP SITRDVSGEG VQQALLKILE G TQASVPPQ GGRKHPHQEF IQIDTTNVLF IVAGAFAGLE KIIYERVGKR GLGFGAEVRS KAEIDTTDHF ADVMPEDLIK FG LIPEFIG RLPVVASVTN LDKESLVKIL SEPKNALVKQ YIRLFEMDGV ELEFTDDALE AIADQAIHRG TGARGLRAIM EEV LLPVMY DIPSRDDVAK VVVTKETVQD NVLPTIVPR

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

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

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 21.543566 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ILPSFIEHSS FGVKESNPYN KLFEERIIFL GVQVDDASAN DIMAQLLVLE SLDPDRDITM YINSPGGGFT SLMAIYDTMQ YVRADIQTV CLGQAASAAA VLLAAGTPGK RMALPNARVL IHQPSLSGVI QGQFSDLEIQ AAEIERMRTL METTLARHTG K DAGVIRKD ...String:
ILPSFIEHSS FGVKESNPYN KLFEERIIFL GVQVDDASAN DIMAQLLVLE SLDPDRDITM YINSPGGGFT SLMAIYDTMQ YVRADIQTV CLGQAASAAA VLLAAGTPGK RMALPNARVL IHQPSLSGVI QGQFSDLEIQ AAEIERMRTL METTLARHTG K DAGVIRKD TDRDKILTAE EAKDYGIIDT VLEYRKLS

UniProtKB: ATP-dependent Clp protease proteolytic subunit 2

-
Macromolecule #3: ATP-dependent Clp protease proteolytic subunit 1

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 19.383111 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SLTDSVYERL LSERIIFLGS EVNDEIANRL CAQILLLAAE DASKDISLYI NSPGGSISAG MAIYDTMVLA PCDIATYAMG MAASMGEFL LAAGTKGKRY ALPHARILMH QPLGGVTGSA ADIAIQAEQF AVIKKEMFRL NAEFTGQPIE RIEADSDRDR W FTAAEALE YGFVDHIITR

UniProtKB: ATP-dependent Clp protease proteolytic subunit 1

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Macromolecule #7: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL...

MacromoleculeName: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
type: ligand / ID: 7 / Number of copies: 14 / Formula: BO2
Molecular weightTheoretical: 384.237 Da
Chemical component information

ChemComp-BO2:
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / medication*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vgq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380684
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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