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- EMDB-71300: Apo form of ClpP1P2 complex from M. tuberculosis -

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Basic information

Entry
Database: EMDB / ID: EMD-71300
TitleApo form of ClpP1P2 complex from M. tuberculosis
Map data
Sample
  • Complex: Tetranary complex of Mtb ClpP1P2 protomers unbound with calprotamide A
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
KeywordsMtb / ClpP / ANTIBIOTIC / HYDROLASE
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytosol
Similarity search - Function
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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBrady SF / Kan J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122559 United States
CitationJournal: To Be Published
Title: Apo form of ClpP1P2 complex from M. tuberculosis
Authors: Brady SF / Kan J
History
DepositionJun 17, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71300.png

Downloads & links

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Map

FileDownload / File: emd_71300.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 256 pix.
= 251.94 Å		0.98 Å/pix.
x 256 pix.
= 251.94 Å		0.98 Å/pix.
x 256 pix.
= 251.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98414 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0215
Minimum - Maximum-0.07764364 - 0.21541959
Average (Standard dev.)0.0002031777 (±0.009443871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 251.93983 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71300_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71300_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71300_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71300_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetranary complex of Mtb ClpP1P2 protomers unbound with calprotamide A

EntireName: Tetranary complex of Mtb ClpP1P2 protomers unbound with calprotamide A
Components
  • Complex: Tetranary complex of Mtb ClpP1P2 protomers unbound with calprotamide A
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1

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Supramolecule #1: Tetranary complex of Mtb ClpP1P2 protomers unbound with calprotamide A

SupramoleculeName: Tetranary complex of Mtb ClpP1P2 protomers unbound with calprotamide A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 91.357 kDa/nm

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Macromolecule #1: ATP-dependent Clp protease proteolytic subunit 2

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.791988 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AGTMNSQNSQ IQPQARYILP SFIEHSSFGV KESNPYNKLF EERIIFLGVQ VDDASANDIM AQLLVLESLD PDRDITMYIN SPGGGFTSL MAIYDTMQYV RADIQTVCLG QAASAAAVLL AAGTPGKRMA LPNARVLIHQ PSLSGVIQGQ FSDLEIQAAE I ERMRTLME ...String:
AGTMNSQNSQ IQPQARYILP SFIEHSSFGV KESNPYNKLF EERIIFLGVQ VDDASANDIM AQLLVLESLD PDRDITMYIN SPGGGFTSL MAIYDTMQYV RADIQTVCLG QAASAAAVLL AAGTPGKRMA LPNARVLIHQ PSLSGVIQGQ FSDLEIQAAE I ERMRTLME TTLARHTGKD AGVIRKDTDR DKILTAEEAK DYGIIDTVLE YRKLSAQTA

UniProtKB: ATP-dependent Clp protease proteolytic subunit 2

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Macromolecule #2: ATP-dependent Clp protease proteolytic subunit 1

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 21.956898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AGTMSQVTDM RSNSQGLSLT DSVYERLLSE RIIFLGSEVN DEIANRLCAQ ILLLAAEDAS KDISLYINSP GGSISAGMAI YDTMVLAPC DIATYAMGMA ASMGEFLLAA GTKGKRYALP HARILMHQPL GGVTGSAADI AIQAEQFAVI KKEMFRLNAE F TGQPIERI ...String:
AGTMSQVTDM RSNSQGLSLT DSVYERLLSE RIIFLGSEVN DEIANRLCAQ ILLLAAEDAS KDISLYINSP GGSISAGMAI YDTMVLAPC DIATYAMGMA ASMGEFLLAA GTKGKRYALP HARILMHQPL GGVTGSAADI AIQAEQFAVI KKEMFRLNAE F TGQPIERI EADSDRDRWF TAAEALEYGF VDHIITRAHV NGEAQ

UniProtKB: ATP-dependent Clp protease proteolytic subunit 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.52 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vgk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2252037
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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