[English] 日本語
Yorodumi
- EMDB-51497: Cryo-EM structure of the multiple peptide resistance factor (MprF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51497
TitleCryo-EM structure of the multiple peptide resistance factor (MprF) from Pseudomonas aeruginosa bound to a synthetic nanobody (Sb29)
Map dataMain Map
Sample
  • Complex: Complex of PaMprF with Sybody29 in Saposin A-protein nanoparticles
    • Complex: Phosphatidylglycerol lysyltransferase
      • Protein or peptide: Phosphatidylglycerol lysyltransferase
    • Complex: Synthetic nanobody (Sybody) 29
      • Protein or peptide: Synthetic nanobody (Sybody) 29
KeywordsLipid Transport / Sybody complex / Antimicrobial Resistance / Saposin-protein Nanoparticle / MEMBRANE PROTEIN
Function / homology
Function and homology information


lysyltransferase / phosphatidylglycerol alanyltransferase activity / phosphatidylglycerol lysyltransferase activity / phospholipid homeostasis / lipid metabolic process / response to antibiotic / plasma membrane
Similarity search - Function
Lysylphosphatidylglycerol synthetase/glycosyltransferase AglD / Lysylphosphatidylglycerol synthase TM region / : / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Phosphatidylglycerol lysyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsHankins MTK / Parrag M / Garaeva AA / Earp JC / Seeger MA / Stansfeld PJ / Bublitz M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust102161/Z/13/Z United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: MprF from is a promiscuous lipid scramblase with broad substrate specificity.
Authors: Matthew T K Hankins / Matyas Parrag / Alisa A Garaeva / Jennifer C Earp / Markus A Seeger / Phillip J Stansfeld / Maike Bublitz /
Abstract: The multiple peptide resistance factor (MprF) is a bifunctional membrane protein found in many bacteria, including and . MprF modifies inner leaflet lipid headgroups through aminoacylation and ...The multiple peptide resistance factor (MprF) is a bifunctional membrane protein found in many bacteria, including and . MprF modifies inner leaflet lipid headgroups through aminoacylation and translocates modified lipid to the outer leaflet. This activity provides increased resistance to antimicrobial agents. MprF presents a promising target in multiresistant pathogens, but structural information is limited and both substrate specificity and energization of MprF-mediated lipid transport are poorly understood. Here, we present the cryo-EM structure of MprF from (MprF) bound to a synthetic nanobody. MprF adopts an "open" conformation with a wide, lipid-exposed groove on the periplasmic side that induces a local membrane deformation in molecular dynamics simulations. Using an in vitro liposome transport assay, we demonstrate that MprF translocates a wide range of different lipids without an external energy source. This suggests that MprF is the first dedicated lipid scramblase to be characterized in bacteria.
History
DepositionSep 5, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51497.png

Downloads & links

-
Map

FileDownload / File: emd_51497.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 358.56 Å		0.83 Å/pix.
x 432 pix.
= 358.56 Å		0.83 Å/pix.
x 432 pix.
= 358.56 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: 0.1
Minimum - Maximum-0.28383923 - 0.5904659
Average (Standard dev.)-0.00038223172 (±0.008798918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 358.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_51497_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_51497_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of PaMprF with Sybody29 in Saposin A-protein nanoparticles

EntireName: Complex of PaMprF with Sybody29 in Saposin A-protein nanoparticles
Components
  • Complex: Complex of PaMprF with Sybody29 in Saposin A-protein nanoparticles
    • Complex: Phosphatidylglycerol lysyltransferase
      • Protein or peptide: Phosphatidylglycerol lysyltransferase
    • Complex: Synthetic nanobody (Sybody) 29
      • Protein or peptide: Synthetic nanobody (Sybody) 29

-
Supramolecule #1: Complex of PaMprF with Sybody29 in Saposin A-protein nanoparticles

SupramoleculeName: Complex of PaMprF with Sybody29 in Saposin A-protein nanoparticles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 112 KDa

-
Supramolecule #2: Phosphatidylglycerol lysyltransferase

SupramoleculeName: Phosphatidylglycerol lysyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

-
Supramolecule #3: Synthetic nanobody (Sybody) 29

SupramoleculeName: Synthetic nanobody (Sybody) 29 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: Phosphatidylglycerol lysyltransferase

MacromoleculeName: Phosphatidylglycerol lysyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysyltransferase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 96.394414 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRTDAPVPEH PAPPSSPASP QRIRLIDRIT AYRQPIGLVF TLLLFGLALV ACYHLLREID PGALHDAIAD VPRPALLGAL SATALGFVI LLGYEWSASR FAGVTLPMRS LATGGFSAFA IGNAVGLSLL SGGSVRYRLY SRHGIGAAEI ARMTLFASLS L GCALPVLA ...String:
MRTDAPVPEH PAPPSSPASP QRIRLIDRIT AYRQPIGLVF TLLLFGLALV ACYHLLREID PGALHDAIAD VPRPALLGAL SATALGFVI LLGYEWSASR FAGVTLPMRS LATGGFSAFA IGNAVGLSLL SGGSVRYRLY SRHGIGAAEI ARMTLFASLS L GCALPVLA ALAALCDLDD AASALHLPRA LVAVIAIAVL SLAVGLVAFL ARHRLPGERP SPDSLLVRLG RRSLRLPGLR LS LLQLLIT ALDVAAAATV LYLLLPETPP FAAFLLVYLL ALAAGVLSHV PGGVGVFEAV LLAAFAGQLG AAPLAAALLL YRL IYVVLP LLLACLLLLF LEARRLWVTR QAIRVASGFA APILAILVFL SGVVLLFSGA TPAIDTRLEH LGFLIPHRLI DASH LVASL IGVLCLLLAQ GLRRRLSAAW ALTLVLLLVG ALLSLLKGFD WEEASLLSLT AALLAMFRRS FYRPSRLMEV PFSPL YVGA SICVVGASVW LLLFANQDVH YSNQLWWQFA LDADAPRALR AALGSCLLLL ALALGWLLRA APPAIREPNA EELQRA ARI IRHSDQPDGG LALTGDKALL FHESDDAFLM YARRGRSMIA LYDPIGPAMQ RAELIWQFRD LCDLHHARPV FYQVRAE NL PFYMDIGLTA LKLGEEARVD LLRFDLENKG KEMKDLRYTW NRGQRDGLAL EFHEPGQAPL DELKAISDAW LGGKQVRE K GFSLGRFTPA YLNFFRIAIV RHQGKPVAFA NLLETDSREL ASLDLMRVHP DAPKLTMEFL MLGLILHYKA QGHARFSLG MVPLAGLQPR RGAPLTQRLG ALVFRRGEQF YNFQGLRRFK DKFQPDWEPR YLAVPAGLDP LVALADTAAL IAGGLTGLVK RLEAL

UniProtKB: Phosphatidylglycerol lysyltransferase

-
Macromolecule #2: Synthetic nanobody (Sybody) 29

MacromoleculeName: Synthetic nanobody (Sybody) 29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.498158 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
GSSSGVQLVE SGGGLVQAGG SLRLSCAASG FPVSSAWMAW YRQAPGKERE WVAAIFSAGQ KTRYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CNVKDTGHWW DIYDYWGQGT QVTVSAGRAG EQKLISEEDL NSAVDHHHHH H

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
80.0 mMpotassium chlorideKCl
2.0 mMmahnesium chlorideMgCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Details: SWISS Model Homology model of a single chain of PDB 7DUW
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111010
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9goe:
Cryo-EM structure of the multiple peptide resistance factor (MprF) from Pseudomonas aeruginosa bound to a synthetic nanobody (Sb29)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more