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- PDB-9nww: Single-particle cryo-EM structure of the first variant of mobiliz... -

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Basic information

Entry
Database: PDB / ID: 9nww
TitleSingle-particle cryo-EM structure of the first variant of mobilized colistin resistance (MCR-1) in its ligand-bound state
Components
  • Fab (MR6) Heavy (H) Chain
  • Fab (MR6) Light (L) Chain
  • Probable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / Membrane protein / phosphoethanolamine transferase / lipid A modification / polymyxin resistance
Function / homology
Function and homology information


lipid A phosphoethanolamine transferase / phosphotransferase activity, phosphate group as acceptor / lipopolysaccharide core region biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Chem-KDL / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZinkle, A.P. / Bunuro-Batista, M. / Herrera, C.M. / Erramilli, S.K. / Kloss, B. / Ashraf, K.U. / Nosol, K. / Zhang, G. / Cater, R.J. / Marty, M.T. ...Zinkle, A.P. / Bunuro-Batista, M. / Herrera, C.M. / Erramilli, S.K. / Kloss, B. / Ashraf, K.U. / Nosol, K. / Zhang, G. / Cater, R.J. / Marty, M.T. / Kossiakoff, A.A. / Trent, M.S. / Nygaard, R. / Stansfeld, P.J. / Mancia, F.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132120 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI181556 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI74416 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI176776 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150098 United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic basis of antimicrobial resistance mediated by the phosphoethanolamine transferase MCR-1.
Authors: Allen P Zinkle / Mariana Bunoro Batista / Carmen M Herrera / Satchal K Erramilli / Brian Kloss / Khuram U Ashraf / Kamil Nosol / Guozhi Zhang / Rosemary J Cater / Michael T Marty / Anthony A ...Authors: Allen P Zinkle / Mariana Bunoro Batista / Carmen M Herrera / Satchal K Erramilli / Brian Kloss / Khuram U Ashraf / Kamil Nosol / Guozhi Zhang / Rosemary J Cater / Michael T Marty / Anthony A Kossiakoff / M Stephen Trent / Rie Nygaard / Phillip J Stansfeld / Filippo Mancia /
Abstract: Polymyxins are used to treat infections caused by multidrug-resistant Gram-negative bacteria. They are cationic peptides that target the negatively charged lipid A component of lipopolysaccharides, ...Polymyxins are used to treat infections caused by multidrug-resistant Gram-negative bacteria. They are cationic peptides that target the negatively charged lipid A component of lipopolysaccharides, disrupting the outer membrane and lysing the cell. Polymyxin resistance is conferred by inner-membrane enzymes, such as phosphoethanolamine transferases, which add positively charged phosphoethanolamine to lipid A. Here, we present the structure of MCR-1, a plasmid-encoded phosphoethanolamine transferase, in its liganded form. The phosphatidylethanolamine donor substrate is bound near the active site in the periplasmic domain, and lipid A is bound over 20 Å away, within the transmembrane region. Integrating structural, biochemical, and drug-resistance data with computational analyses, we propose a two-state model in which the periplasmic domain rotates to bring the active site to lipid A, near the preferential phosphate modification site for MCR-1. This enzymatic mechanism may be generally applicable to other phosphoform transferases with large, globular soluble domains.
History
DepositionMar 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable phosphatidylethanolamine transferase Mcr-1
C: Fab (MR6) Light (L) Chain
D: Fab (MR6) Heavy (H) Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2805
Polymers112,2973
Non-polymers2,9832
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Probable phosphatidylethanolamine transferase Mcr-1 / Polymyxin resistance protein MCR-1


Mass: 63996.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Antibody Fab (MR6) Light (L) Chain


Mass: 23330.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab (MR6) Heavy (H) Chain


Mass: 24969.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-KDL / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 2238.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C110H202N2O39P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
Has ligand of interestY
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: PE- and KLA-bound MCR-1 complex with Fab fragment / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.137 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 58.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32882 / Symmetry type: POINT
RefinementHighest resolution: 3.58 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026190
ELECTRON MICROSCOPYf_angle_d0.5888402
ELECTRON MICROSCOPYf_dihedral_angle_d12.629932
ELECTRON MICROSCOPYf_chiral_restr0.042951
ELECTRON MICROSCOPYf_plane_restr0.0041040

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