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- EMDB-49896: Single-particle cryo-EM structure of the first variant of mobiliz... -

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Entry
Database: EMDB / ID: EMD-49896
TitleSingle-particle cryo-EM structure of the first variant of mobilized colistin resistance (MCR-1) in its ligand-bound state
Map dataSingle-particle cryo-EM structure of the first variant of mobilized colistin resistance (MCR-1) in its ligand-bound state
Sample
  • Complex: PE- and KLA-bound MCR-1 complex with Fab fragment
    • Protein or peptide: Probable phosphatidylethanolamine transferase Mcr-1
    • Protein or peptide: Fab (MR6) Light (L) Chain
    • Protein or peptide: Fab (MR6) Heavy (H) Chain
  • Ligand: (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
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
KeywordsMembrane protein / phosphoethanolamine transferase / lipid A modification / polymyxin resistance / TRANSFERASE
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
Phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZinkle AP / Bunuro-Batista M / Herrera CM / Erramilli SK / Kloss B / Ashraf KU / Nosol K / Zhang G / Cater RJ / Marty MT ...Zinkle AP / Bunuro-Batista M / Herrera CM / Erramilli SK / Kloss B / Ashraf KU / Nosol K / Zhang G / Cater RJ / Marty MT / Kossiakoff AA / Trent MS / Nygaard R / Stansfeld PJ / Mancia F
Funding support United States, 5 items
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, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49896.png

Downloads & links

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Map

FileDownload / File: emd_49896.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle cryo-EM structure of the first variant of mobilized colistin resistance (MCR-1) in its ligand-bound state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.63223207 - 0.98073274
Average (Standard dev.)0.000126707 (±0.021711394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49896_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49896_half_map_2.map
AnnotationHalf 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 : PE- and KLA-bound MCR-1 complex with Fab fragment

EntireName: PE- and KLA-bound MCR-1 complex with Fab fragment
Components
  • Complex: PE- and KLA-bound MCR-1 complex with Fab fragment
    • Protein or peptide: Probable phosphatidylethanolamine transferase Mcr-1
    • Protein or peptide: Fab (MR6) Light (L) Chain
    • Protein or peptide: Fab (MR6) Heavy (H) Chain
  • Ligand: (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
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

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Supramolecule #1: PE- and KLA-bound MCR-1 complex with Fab fragment

SupramoleculeName: PE- and KLA-bound MCR-1 complex with Fab fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 137 KDa

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Macromolecule #1: Probable phosphatidylethanolamine transferase Mcr-1

MacromoleculeName: Probable phosphatidylethanolamine transferase Mcr-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 63.996855 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHHHH HSSGVDLGTE NLYFQSNAGG GSGGGSMMQH TSVWYRRSVS PFVLVASVAV FLTATANLTF FDKISQTYPI ADNLGFVLT IAVVLFGAML LITTLLSSYR YVLKPVLILL LIMGAVTSYF TDTYGTVYDT TMLQNALQTD QAETKDLLNA A FIMRIIGL ...String:
MHHHHHHHHH HSSGVDLGTE NLYFQSNAGG GSGGGSMMQH TSVWYRRSVS PFVLVASVAV FLTATANLTF FDKISQTYPI ADNLGFVLT IAVVLFGAML LITTLLSSYR YVLKPVLILL LIMGAVTSYF TDTYGTVYDT TMLQNALQTD QAETKDLLNA A FIMRIIGL GVLPSLLVAF VKVDYPTWGK GLMRRLGLIV ASLALILLPV VAFSSHYASF FRVHKPLRSY VNPIMPIYSV GK LASIEYK KASAPKDTIY HAKDAVQATK PDMRKPRLVV FVVGETARAD HVSFNGYERD TFPQLAKIDG VTNFSNVTSC GTS TAYSVP CMFSYLGADE YDVDTAKYQE NVLDTLDRLG VSILWRDNNS DSKGVMDKLP KAQFADYKSA TNNAICNTNP YNEC RDVGM LVGLDDFVAA NNGKDMLIML HQMGNHGPAY FKRYDEKFAK FTPVCEGNEL AKCEHQSLIN AYDNALLATD DFIAQ SIQW LQTHSNAYDV SMLYVSDHGE SLGENGVYLH GMPNAFAPKE QRSVPAFFWT DKQTGITPMA TDTVLTHDAI TPTLLK LFD VTADKVKDRT AFIR

UniProtKB: Phosphatidylethanolamine transferase Mcr-1

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Macromolecule #2: Fab (MR6) Light (L) Chain

MacromoleculeName: Fab (MR6) Light (L) Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.330891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYWPITFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYWPITFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: Fab (MR6) Heavy (H) Chain

MacromoleculeName: Fab (MR6) Heavy (H) Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.969709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYYSSIHWV RQAPGKGLEW VASIYSSYSS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ASGNFSSWWS HGWYALYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYYSSIHWV RQAPGKGLEW VASIYSSYSS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ASGNFSSWWS HGWYALYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTHT

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Macromolecule #4: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(...

MacromoleculeName: (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- ...Name: (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
type: ligand / ID: 4 / Number of copies: 1 / Formula: KDL
Molecular weightTheoretical: 2.238718 KDa
Chemical component information

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

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Macromolecule #5: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 5 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.2 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32882
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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