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- PDB-9dvb: Thermus thermophilus MreC-MreD complex with an internal MreD BRIL... -

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Basic information

Entry
Database: PDB / ID: 9dvb
TitleThermus thermophilus MreC-MreD complex with an internal MreD BRIL fusion and an anti-BRIL Fab
Components
  • BAG2 anti-BRIL Fab heavy chain
  • BAG2 anti-BRIL Fab light chain
  • Cell shape-determining protein MreC
  • Rod shape-determining protein MreD
  • Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Peptidoglycan synthesis regulator / S-component fold / Rod complex / SEDS activator
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 speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGilman, M.S.A. / Kruse, A.C.
Funding support United States, 9items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Soluble cytochrome b562
C: Cell shape-determining protein MreC
D: Rod shape-determining protein MreD
H: BAG2 anti-BRIL Fab heavy chain
L: BAG2 anti-BRIL Fab light chain
N: Soluble cytochrome b562
O: Cell shape-determining protein MreC
P: Rod shape-determining protein MreD
W: BAG2 anti-BRIL Fab heavy chain
X: BAG2 anti-BRIL Fab light chain


Theoretical massNumber of molelcules
Total (without water)210,09710
Polymers210,09710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 12760.479 Da / Num. of mol.: 2 / Fragment: BRIL domain, residues 30-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Protein Cell shape-determining protein MreC / Cell shape protein MreC


Mass: 27798.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHB5018_12720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7R7YII3
#3: Protein Rod shape-determining protein MreD


Mass: 16668.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA1190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJ24
#4: Antibody BAG2 anti-BRIL Fab heavy chain


Mass: 24279.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#5: Antibody BAG2 anti-BRIL Fab light chain


Mass: 23541.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex containing two copies of TtMreC and TtMreD-BRIL with two BAG2 anti-BRIL Fabs bound.
Type: COMPLEX
Details: Complex formed by two copies of Thermus thermophilus MreC and two copies of Thermus thermophilus MreD fused internally with a BRIL domain. Two copies of the BAG2 anti-BRIL Fab with hinge- ...Details: Complex formed by two copies of Thermus thermophilus MreC and two copies of Thermus thermophilus MreD fused internally with a BRIL domain. Two copies of the BAG2 anti-BRIL Fab with hinge-stabilizing mutations in the heavy chain.
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Thermus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166346 / Symmetry type: POINT

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