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- EMDB-60898: cryo-EM structure of FtsE/X and ZipA complex in filament -

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Basic information

Entry
Database: EMDB / ID: EMD-60898
Titlecryo-EM structure of FtsE/X and ZipA complex in filament
Map data
Sample
  • Complex: complex of FtsE/X-ZipA in filament
    • Protein or peptide: Cell division protein ZipA
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Keywordscell division / division filament / FtsE/X / ZipA / CELL CYCLE
Function / homology
Function and homology information


division septum / divisome complex / Gram-negative-bacterium-type cell wall / signal recognition particle binding / peptidoglycan turnover / plasma membrane protein complex / SRP-dependent cotranslational protein targeting to membrane / division septum assembly / FtsZ-dependent cytokinesis / cell division site ...division septum / divisome complex / Gram-negative-bacterium-type cell wall / signal recognition particle binding / peptidoglycan turnover / plasma membrane protein complex / SRP-dependent cotranslational protein targeting to membrane / division septum assembly / FtsZ-dependent cytokinesis / cell division site / ATPase complex / positive regulation of cell division / cell division / GTPase activity / GTP binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / : / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain ...ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / : / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / Signal-recognition particle receptor FtsY / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ABC transporter-like, conserved site / ABC transporters family signature. / 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 protein ZipA / Cell division ATP-binding protein FtsE
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhu KF / Li JW / Luo M
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: To Be Published
Title: cryo-EM structure of FtsE/X and ZipA complex in filament
Authors: Zhu KF / Li JW / Luo M
History
DepositionJul 20, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60898.png

Downloads & links

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Map

FileDownload / File: emd_60898.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.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.123
Minimum - Maximum-0.84669983 - 1.7637507
Average (Standard dev.)0.0003754357 (±0.024354419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60898_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_60898_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 : complex of FtsE/X-ZipA in filament

EntireName: complex of FtsE/X-ZipA in filament
Components
  • Complex: complex of FtsE/X-ZipA in filament
    • Protein or peptide: Cell division protein ZipA
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: complex of FtsE/X-ZipA in filament

SupramoleculeName: complex of FtsE/X-ZipA in filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Macromolecule #1: Cell division protein ZipA

MacromoleculeName: Cell division protein ZipA / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 36.517199 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMQDLRLILI IVGAIAIIAL LVHGFWTSRK ERSSMFRDRP LKRMKSKRDD DSYDEDVEDD EGVGEVRVHR VNHAPANAQE HEAARPSPQ HQYQPPYASA QPRQPVQQPP EAQVPPQHAP HPAQPVQQPA YQPQPEQPLQ QPVSPQVAPA PQPVHSAPQP A QQAFQPAE ...String:
MMQDLRLILI IVGAIAIIAL LVHGFWTSRK ERSSMFRDRP LKRMKSKRDD DSYDEDVEDD EGVGEVRVHR VNHAPANAQE HEAARPSPQ HQYQPPYASA QPRQPVQQPP EAQVPPQHAP HPAQPVQQPA YQPQPEQPLQ QPVSPQVAPA PQPVHSAPQP A QQAFQPAE PVAAPQPEPV AEPAPVMDKP KRKEAVIIMN VAAHHGSELN GELLLNSIQQ AGFIFGDMNI YHRHLSPDGS GP ALFSLAN MVKPGTFDPE MKDFTTPGVT IFMQVPSYGD ELQNFKLMLQ SAQHIADEVG GVVLDDQRRM MTPQKLREYQ DII REVKDA NA

UniProtKB: Cell division protein ZipA

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Macromolecule #2: Cell division ATP-binding protein FtsE

MacromoleculeName: Cell division ATP-binding protein FtsE / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 24.832695 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SGLVMIRFEH VSKAYLGGRQ ALQGVTFHMQ PGEMAFLTGH SGAGKSTLLK LICGIERPSA GKIWFSGHDI TRLKNREVPF LRRQIGMIF QDHHLLMDRT VYDNVAIPLI IAGASGDDIR RRVSAALDKV GLLDKAKNFP IQLSGGEQQR VGIARAVVNK P AVLLADEP ...String:
SGLVMIRFEH VSKAYLGGRQ ALQGVTFHMQ PGEMAFLTGH SGAGKSTLLK LICGIERPSA GKIWFSGHDI TRLKNREVPF LRRQIGMIF QDHHLLMDRT VYDNVAIPLI IAGASGDDIR RRVSAALDKV GLLDKAKNFP IQLSGGEQQR VGIARAVVNK P AVLLADEP TGNLDDALSE GILRLFEEFN RVGVTVLMAT HDINLISRRS YRMLTLSDGH LHGGVGHE

UniProtKB: Cell division ATP-binding protein FtsE

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Macromolecule #3: Cell division protein FtsX

MacromoleculeName: Cell division protein FtsX / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 38.5835 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNKRDAINHI RQFGGRLDRF RKSVGGSGDG GRNAPKRAKS SPKPVNRKTN VFNEQVRYAF HGALQDLKSK PFATFLTVMV IAISLTLPS VCYMVYKNVN QAATQYYPSP QITVYLQKTL DDDAAAGVVA QLQAEQGVEK VNYLSREDAL GEFRNWSGFG G ALDMLEEN ...String:
MNKRDAINHI RQFGGRLDRF RKSVGGSGDG GRNAPKRAKS SPKPVNRKTN VFNEQVRYAF HGALQDLKSK PFATFLTVMV IAISLTLPS VCYMVYKNVN QAATQYYPSP QITVYLQKTL DDDAAAGVVA QLQAEQGVEK VNYLSREDAL GEFRNWSGFG G ALDMLEEN PLPAVAVVIP KLDFQGTESL NTLRDRITQI NGIDEVRMDD SWFARLAALT GLVGRVSAMI GVLMVAAVFL VI GNSVRLS IFARRDSINV QKLIGATDGF ILRPFLYGGA LLGFSGALLS LILSEILVLR LSSAVAEVAQ VFGTKFDING LSF DECLLL LLVCSMIGWV AAWLATVQHL RHFTPE

UniProtKB: Cell division protein FtsX

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 18 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

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

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 36.65 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #2 - Average electron dose: 36.65 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8w6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194215
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Image processing #2

Image processing ID2
Image recording ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8w6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194215

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Image processing #3

Image processing ID3
Image recording ID3
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8w6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194215

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Image processing #4

Image processing ID4
Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8w6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194215
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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