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- EMDB-52765: Structure of the Mycobacterium tuberculosis ClpC1P1P2 complex bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-52765
TitleStructure of the Mycobacterium tuberculosis ClpC1P1P2 complex bound to the activator Bz-LL - consensus map
Map data
Sample
  • Complex: ClpC1P1P2
    • Protein or peptide: ClpC1
    • Protein or peptide: ClpP1
    • Protein or peptide: ClpP2
Keywordsprotein quality control / peptide activator / protease / ATPase / CHAPERONE
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsSemchonok D / Weinhaeupl K / Gragera M / Arranz R / Bueno Carrasco MT / Fraga H
Funding support1 items
OrganizationGrant numberCountry
Other governmentInstruct-ERIC 30641, 26164
CitationJournal: To Be Published
Title: Structure of the Mycobacterium tuberculosis ClpC1P1P2 complex bound to the activator Bz-LL
Authors: Weinhaeupl K / Semchonok DA / Gragera M / Arranz R / Bueno Carrasco MT / Fraga H
History
DepositionFeb 7, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_52765.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.525 Å
Density
Contour LevelBy AUTHOR: 0.0229
Minimum - Maximum-0.06892664 - 0.15968274
Average (Standard dev.)0.00009015077 (±0.006577393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ClpC1P1P2

EntireName: ClpC1P1P2
Components
  • Complex: ClpC1P1P2
    • Protein or peptide: ClpC1
    • Protein or peptide: ClpP1
    • Protein or peptide: ClpP2

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Supramolecule #1: ClpC1P1P2

SupramoleculeName: ClpC1P1P2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: ClpC1

MacromoleculeName: ClpC1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFERFTDRAR RVVVLAQEEA RMLNHNYIGT EHILLGLIHE GEGVAAKSLE SLGISLEGVR SQVEEIIGQ GQQAPSGHIP FTPRAKKVLE LSLREALQLG HNYIGTEHIL LGLIREGEGV A AQVLVKLG AELTRVRQQV IQLLSGYQGK EAAEAGTGGR GGESGSPSTS ...String:
MFERFTDRAR RVVVLAQEEA RMLNHNYIGT EHILLGLIHE GEGVAAKSLE SLGISLEGVR SQVEEIIGQ GQQAPSGHIP FTPRAKKVLE LSLREALQLG HNYIGTEHIL LGLIREGEGV A AQVLVKLG AELTRVRQQV IQLLSGYQGK EAAEAGTGGR GGESGSPSTS LVLDQFGRNL TA AAMEGKL DPVIGREKEI ERVMQVLSRR TKNNPVLIGE PGVGKTAVVE GLAQAIVHGE VPE TLKDKQ LYTLDLGSLV AGSRYRGDFE ERLKKVLKEI NTRGDIILFI DELHTLVGAG AAEG AIDAA SILKPKLARG ELQTIGATTL DEYRKYIEKD AALERRFQPV QVGEPTVEHT IEILK GLRD RYEAHHRVSI TDAAMVAAAT LADRYINDRF LPDKAIDLID EAGARMRIRR MTAPPD LRE FDEKIAEARR EKESAIDAQD AEKAASLRDR EKTLVAQRAE REKQWRSGDL DVVAEVD DE QIAEVLGNWT GIPVFKLTEA ETTRLLRMEE ELHKRIIGQE DAVKAVSKAI RRTRAGLK D PKRPSGSFIF AGPSGVGKTE LSKALANFLF GDDDALIQID MGEFHDRFTA SRLFGAPPG YVGYEEGGQL TEKVRRKPFS VVLFDEIEKA HQEIYNSLLQ VLEDGRLTDG QGRTVDFKNT VLIFTSNLG TSDISKPVGL GFSKGGGEND YERMKQKVND ELKKHFRPEF LNRIDDIIVF H QLTREEII RMVDLMISRV AGQLKSKDMA LVLTDAAKAL LAKRGFDPVL GARPLRRTIQ RE IEDQLSE KILFEEVGPG QVVTVDVDNW DGEGPGEDAV FTFTGTRKPP AEPDLAKAGA HSA GGPEPA AR

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Macromolecule #2: ClpP1

MacromoleculeName: ClpP1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQVTDMRSN SQGLSLTDSV YERLLSERII FLGSEVNDEI ANRLCAQILL LAAEDASKDI SLYINSPGGS ISAGMAIYDT MVLAPCDIAT YAMGMAASMG EFLLAAGTKG KRYALPHARI LMHQPLGGVT GSAADIAIQA EQFAVIKKEM FRLNAEFTGQ PIERIEADSD ...String:
MSQVTDMRSN SQGLSLTDSV YERLLSERII FLGSEVNDEI ANRLCAQILL LAAEDASKDI SLYINSPGGS ISAGMAIYDT MVLAPCDIAT YAMGMAASMG EFLLAAGTKG KRYALPHARI LMHQPLGGVT GSAADIAIQA EQFAVIKKEM FRLNAEFTGQ PIERIEADSD RDRWFTAAEA LEYGFVDHII TRAHVNGEAQ

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Macromolecule #3: ClpP2

MacromoleculeName: ClpP2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSQNSQIQP QARYILPSFI EHSSFGVKES NPYNKLFEER IIFLGVQVDD ASANDIMAQL LVLESLDPDR DITMYINSPG GGFTSLMAIY DTMQYVRADI QTVCLGQAAS AAAVLLAAGT PGKRMALPNA RVLIHQPSLS GVIQGQFSDL EIQAAEIERM RTLMETTLAR ...String:
MNSQNSQIQP QARYILPSFI EHSSFGVKES NPYNKLFEER IIFLGVQVDD ASANDIMAQL LVLESLDPDR DITMYINSPG GGFTSLMAIY DTMQYVRADI QTVCLGQAAS AAAVLLAAGT PGKRMALPNA RVLIHQPSLS GVIQGQFSDL EIQAAEIERM RTLMETTLAR HTGKDAGVIR KDTDRDKILT AEEAKDYGII DTVLEYRKLS AQTA

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 77.0 K / Max: 77.0 K
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 10943 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1372648
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 10 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 71218
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 15000 / Software - Name: cryoSPARC (ver. 4.6.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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