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- EMDB-35364: Cryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/R... -

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Basic information

Entry
Database: EMDB / ID: EMD-35364
TitleCryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/RipC complex in peptidisc
Map data
Sample
  • Complex: complex of FtsEX-RipC-ATP
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
    • Protein or peptide: Probable endopeptidase MT2245
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscomplex / TRANSPORT PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / transmembrane transporter activity / cysteine-type peptidase activity / transmembrane transport / manganese ion binding / cell division / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
: / : / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / ABC transporter, lipoprotein release, LolD ...: / : / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / Papain-like cysteine peptidase superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell division protein FtsX / Cell division ATP-binding protein FtsE / Probable endopeptidase MT2245
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLi J / Xu X / Luo M
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)A-0008412-00-00 Singapore
CitationJournal: Nat Commun / Year: 2023
Title: Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis.
Authors: Jianwei Li / Xin Xu / Jian Shi / Juan A Hermoso / Lok-To Sham / Min Luo /
Abstract: The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX ...The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX system directly activates peptidoglycan-hydrolases by a mechanism that remains unclear. Here we report our investigation of Mycobacterium tuberculosis FtsEX as a non-canonical regulator with high basal ATPase activity. The cryo-EM structures of the FtsEX system alone and in complex with RipC, as well as the ATP-activated state, unveil detailed information on the signal transduction mechanism, leading to the activation of RipC. Our findings indicate that RipC is recognized through a "Match and Fit" mechanism, resulting in an asymmetric rearrangement of the extracellular domains of FtsX and a unique inclined binding mode of RipC. This study provides insights into the molecular mechanisms of FtsEX and RipC regulation in the context of a critical human pathogen, guiding the design of drugs targeting peptidoglycan remodeling.
History
DepositionFeb 12, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35364.png

Downloads & links

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Map

FileDownload / File: emd_35364.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.141
Minimum - Maximum-0.29086494 - 0.66952103
Average (Standard dev.)0.00010607909 (±0.015175993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35364_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35364_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : complex of FtsEX-RipC-ATP

EntireName: complex of FtsEX-RipC-ATP
Components
  • Complex: complex of FtsEX-RipC-ATP
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
    • Protein or peptide: Probable endopeptidase MT2245
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: complex of FtsEX-RipC-ATP

SupramoleculeName: complex of FtsEX-RipC-ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: Cell division ATP-binding protein FtsE

MacromoleculeName: Cell division ATP-binding protein FtsE / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 25.766697 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MMITLDHVTK QYKSSARPAL DDINVKIDKG EFVFLIGPSG SGKSTFMRLL LAAETPTSGD VRVSKFHVNK LRGRHVPKLR QVIGCVFQD FRLLQQKTVY DNVAFALEVI GKRTDAINRV VPEVLETVGL SGKANRLPDE LSGGEQQRVA IARAFVNRPL V LLADEPTG ...String:
MMITLDHVTK QYKSSARPAL DDINVKIDKG EFVFLIGPSG SGKSTFMRLL LAAETPTSGD VRVSKFHVNK LRGRHVPKLR QVIGCVFQD FRLLQQKTVY DNVAFALEVI GKRTDAINRV VPEVLETVGL SGKANRLPDE LSGGEQQRVA IARAFVNRPL V LLADEPTG NLDPETSRDI MDLLERINRT GTTVLMATHD HHIVDSMRQR VVELSLGRLV RDEQRGVYGM DR

UniProtKB: Cell division ATP-binding protein FtsE

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Macromolecule #2: Cell division protein FtsX

MacromoleculeName: Cell division protein FtsX / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 32.851355 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MRFGFLLNEV LTGFRRNVTM TIAMILTTAI SVGLFGGGML VVRLADSSRA IYLDRVESQV FLTEDVSAND SSCDTTACKA LREKIETRS DVKAVRFLNR QQAYDDAIRK FPQFKDVAGK DSFPASFIVK LENPEQHKDF DTAMKGQPGV LDVLNQKELI D RLFAVLDG ...String:
MRFGFLLNEV LTGFRRNVTM TIAMILTTAI SVGLFGGGML VVRLADSSRA IYLDRVESQV FLTEDVSAND SSCDTTACKA LREKIETRS DVKAVRFLNR QQAYDDAIRK FPQFKDVAGK DSFPASFIVK LENPEQHKDF DTAMKGQPGV LDVLNQKELI D RLFAVLDG LSNAAFAVAL VQAIGAILLI ANMVQVAAYT RRTEIGIMRL VGASRWYTQL PFLVEAMLAA TMGVGIAVAG LM VVRALFL ENALNQFYQA NLIAKVDYAD ILFITPWLLL LGVAMSGLTA YLTLRLYVRR

UniProtKB: Cell division protein FtsX

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Macromolecule #3: Probable endopeptidase MT2245

MacromoleculeName: Probable endopeptidase MT2245 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 39.792918 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MRLDQRWLIA RVIMRSAIGF FASFTVSSGV LAANVLADPA DDALAKLNEL SRQAEQTTEA LHSAQLDLNE KLAAQRAADQ KLADNRTAL DAARARLATF QTAVNKVAAA TYMGGRTHGM DAILTAESPQ LLIDRLSVQR VMAHQMSTQM ARFKAAGEQA V KAEQAAAK ...String:
MRLDQRWLIA RVIMRSAIGF FASFTVSSGV LAANVLADPA DDALAKLNEL SRQAEQTTEA LHSAQLDLNE KLAAQRAADQ KLADNRTAL DAARARLATF QTAVNKVAAA TYMGGRTHGM DAILTAESPQ LLIDRLSVQR VMAHQMSTQM ARFKAAGEQA V KAEQAAAK SAADARSAAE QAAAVRANLQ HKQSQLQVQI AVVKSQYVAL TPEERTALAD PGPVPAVAAI APGAPPAALP PG APPGDGP APGVAPPPGG MPGLPFVQPD GAGGDRTAVV QAALTQVGAP YAWGGAAPGG FDCSGLVMWA FQQAGIALPH SSQ ALAHGG QPVALSDLQP GDVLTFYSDA SHAGIYIGDG LMVHSSTYGV PVRVVPMDSS GPIYDARRY

UniProtKB: Probable endopeptidase MT2245

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 6.02 sec. / Average electron dose: 38.837 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111341
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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