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- EMDB-47200: Thermus thermophilus MreC-MreD complex with a C-terminal MreD BRI... -

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Basic information

Entry
Database: EMDB / ID: EMD-47200
TitleThermus thermophilus MreC-MreD complex with a C-terminal MreD BRIL fusion and an anti-BRIL Fab.
Map dataMreC and MreD with an C-terminal BRIL fusion and anti-BRIL Fab
Sample
  • Complex: Complex containing two copies of TtMreC and TtMreD-BRIL with one BAG2 anti-BRIL Fab.
    • Protein or peptide: Soluble cytochrome b562
    • Protein or peptide: Cell shape-determining protein MreC
    • Protein or peptide: Rod shape-determining protein MreD
    • Protein or peptide: BAG2 anti-BRIL Fab heavy chain
    • Protein or peptide: BAG2 anti-BRIL Fab light chain
KeywordsPeptidoglycan synthesis regulator / S-component fold / Rod complex / SEDS activator / MEMBRANE PROTEIN
Function / homology
Function and homology information


electron transport chain / regulation of cell shape / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cell shape-determining protein MreD / rod shape-determining protein MreD / : / Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / Rod shape-determining protein MreC, barrel core / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Cell shape-determining protein MreC / Soluble cytochrome b562 / Rod shape-determining protein MreD
Similarity search - Component
Biological speciesThermus thermophilus (bacteria) / Escherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsGilman MSA / Kruse AC
Funding support United States, 9 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Investigator Funds United States
Howard Hughes Medical Institute (HHMI)Hanna H. Gray Fellows program United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI158028 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM114065 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083365 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM135519 United States
National Science Foundation (NSF, United States)Graduate Research Fellowship Award United States
Other privateVan Maanen Fellowship from the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School United States
Other privateInnovation Research Fund of the Dana-Farber Cancer Institute United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Conformational regulation of two essential activators of bacterial cell elongation.
Authors: Morgan S A Gilman / Irina Shlosman / Daniel D Samé Guerra / Masy Domecillo / Elayne M Fivenson / Claire Bourett / Thomas G Bernhardt / Nicholas F Polizzi / Joseph J Loparo / Andrew C Kruse /
Abstract: The peptidoglycan (PG) cell wall is critical for bacterial growth and survival and is a primary antibiotic target. MreD is an essential accessory factor of the Rod complex, which carries out PG ...The peptidoglycan (PG) cell wall is critical for bacterial growth and survival and is a primary antibiotic target. MreD is an essential accessory factor of the Rod complex, which carries out PG synthesis during elongation, yet little is known about how MreD facilitates this process. Here, we present the cryoelectron microscopy structure of MreD in complex with another essential Rod complex component, MreC. The structure reveals that a periplasmic-facing pocket of MreD interacts with multiple membrane-proximal regions of MreC. We use single-molecule FRET to show that MreD controls the conformation of MreC through these contacts, inducing a state primed for Rod complex activation. Using as a model, we demonstrate that disrupting these interactions abolishes Rod complex activity in vivo. Our findings reveal the role of MreD in bacterial cell shape determination and highlight its potential as an antibiotic target.
History
DepositionOct 7, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47200.png

Downloads & links

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Map

FileDownload / File: emd_47200.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMreC and MreD with an C-terminal BRIL fusion and anti-BRIL Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.3101185 - 0.6461523
Average (Standard dev.)0.00055377005 (±0.018031422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: MreC and MreD with an C-terminal BRIL fusion...

Fileemd_47200_half_map_1.map
AnnotationMreC and MreD with an C-terminal BRIL fusion and anti-BRIL Fab, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MreC and MreD with an C-terminal BRIL fusion...

Fileemd_47200_half_map_2.map
AnnotationMreC and MreD with an C-terminal BRIL fusion and anti-BRIL Fab, half map A
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 containing two copies of TtMreC and TtMreD-BRIL with one ...

EntireName: Complex containing two copies of TtMreC and TtMreD-BRIL with one BAG2 anti-BRIL Fab.
Components
  • Complex: Complex containing two copies of TtMreC and TtMreD-BRIL with one BAG2 anti-BRIL Fab.
    • Protein or peptide: Soluble cytochrome b562
    • Protein or peptide: Cell shape-determining protein MreC
    • Protein or peptide: Rod shape-determining protein MreD
    • Protein or peptide: BAG2 anti-BRIL Fab heavy chain
    • Protein or peptide: BAG2 anti-BRIL Fab light chain

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Supramolecule #1: Complex containing two copies of TtMreC and TtMreD-BRIL with one ...

SupramoleculeName: Complex containing two copies of TtMreC and TtMreD-BRIL with one BAG2 anti-BRIL Fab.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Complex formed by two copies of Thermus thermophilus MreC and two copies of Thermus thermophilus MreD fused at the C-terminus with a BRIL domain. One copy of the BAG2 anti-BRIL Fab with ...Details: Complex formed by two copies of Thermus thermophilus MreC and two copies of Thermus thermophilus MreD fused at the C-terminus with a BRIL domain. One copy of the BAG2 anti-BRIL Fab with hinge-stabilizing mutations in the heavy chain.
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #1: Soluble cytochrome b562

MacromoleculeName: Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.760479 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HAAVAAAEAT IKPAFETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANE GKVKEAQAAA EQLKTTLAEL QKRYWART

UniProtKB: Soluble cytochrome b562

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Macromolecule #2: Cell shape-determining protein MreC

MacromoleculeName: Cell shape-determining protein MreC / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 27.798629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MREHLLPRFL LALLLALGLA LAALTRPLAP GFALSFSPLT AFPLHLGHRL GQNLRAAWSA LSARQDLLAE NQRLKEEVAR LTTENARLR LEVARLARAL EVKAGQAPGV VAVAPVVAED ASGLYRRLVL GLGSQDGLRP GMPVTAPQGL VGLVVEVEAH R ALVRTLLD ...String:
MREHLLPRFL LALLLALGLA LAALTRPLAP GFALSFSPLT AFPLHLGHRL GQNLRAAWSA LSARQDLLAE NQRLKEEVAR LTTENARLR LEVARLARAL EVKAGQAPGV VAVAPVVAED ASGLYRRLVL GLGSQDGLRP GMPVTAPQGL VGLVVEVEAH R ALVRTLLD PESRVGVRVG EKPGRGVARG APPGLLVAEF PPTVAVAPGD LLLTGATLGL FPDGIPVGRV ERVERAQGGL KV RAWARPL VDLSLLEEVV VLRPL

UniProtKB: Cell shape-determining protein MreC

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Macromolecule #3: Rod shape-determining protein MreD

MacromoleculeName: Rod shape-determining protein MreD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 16.668936 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALVYLVLLL FLSGLLQALL PEGWPAPDLF LVYALWLAAS RPPLLGLALA FLVGLLQDLL GFGLLGLHAV GLLLAAYAYY GAARYLDLR SPAGALAAFA LAFLGKWFGY FLVAYWLRLD LPALFPWLPL GEGLLSLAFF WPLRPKAREE PKA

UniProtKB: Rod shape-determining protein MreD

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Macromolecule #4: BAG2 anti-BRIL Fab heavy chain

MacromoleculeName: BAG2 anti-BRIL Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.279115 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNVV DFSLHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVFNQIKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNVV DFSLHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVFNQIKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCD

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Macromolecule #5: BAG2 anti-BRIL Fab light chain

MacromoleculeName: BAG2 anti-BRIL Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.541164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio model generated using cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51857
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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