[English] 日本語
Yorodumi
- EMDB-65649: MprF from Pseudomonas aeruginosa mutant, H566C in nanodisc, C2 sy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65649
TitleMprF from Pseudomonas aeruginosa mutant, H566C in nanodisc, C2 symmetry
Map dataFull map of PaMprF H566C in nanodisc
Sample
  • Complex: MprF dimer
    • Protein or peptide: Phosphatidylglycerol lysyltransferase
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsMultiple peptide resistance factor / Membrane Enzyme / Synthase / Flippase / aminoacylated lipid / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphatidylglycerol alanyltransferase activity / lysyltransferase / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJha S / Vinothkumar KR
Funding support India, 2 items
OrganizationGrant numberCountry
Other governmentDepartment of Atomic Energy, Government of India, RTI 4006 India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: FEBS J / Year: 2026
Title: Cryo-EM structures of multiple-peptide resistance factor (MprF) from Pseudomonas aeruginosa.
Authors: Shaileshanand Jha / Kutti R Vinothkumar /
Abstract: Aminoacylation of the lipid head group in many bacteria is carried out by bi-functional enzymes called MprF, which encode a soluble synthase domain that typically transfers lysine or alanine from a ...Aminoacylation of the lipid head group in many bacteria is carried out by bi-functional enzymes called MprF, which encode a soluble synthase domain that typically transfers lysine or alanine from a tRNA to lipid head groups. The modified lipid is subsequently translocated across the leaflets by a transmembrane domain. This modification of lipids probably evolved to adapt to the environment where the microbes reside. Here, we describe the cryo-EM structures of MprF enzyme from Pseudomonas aeruginosa, revealing a dimeric enzyme with a distinct architecture when compared with the homologous Rhizobium enzymes, and validate this arrangement with biochemical analyses. The cryo-EM maps and the models in detergent micelle and nanodisc reveal a conformational change of the terminal helix of the synthase domain, highlighting the dynamic elements in the enzyme that might facilitate catalysis. Several lipid-like densities are observed in the cryo-EM maps, which might indicate the path taken by the lipids, coupling the function of the two domains. The structures allow postulation of the binding modes of tRNA and lipid transport, and suggest that the mobile secondary structural elements in the synthase domain might play a mechanistic role in these functions.
History
DepositionAug 1, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65649.png

Downloads & links

-
Map

FileDownload / File: emd_65649.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of PaMprF H566C in nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.7905964 - 2.3255394
Average (Standard dev.)-0.0011872691 (±0.060980577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65649_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of PaMprF H566C in nanodisc

Fileemd_65649_half_map_1.map
AnnotationHalf map 1 of PaMprF H566C in nanodisc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of PaMprF H566C in nanodisc

Fileemd_65649_half_map_2.map
AnnotationHalf map 2 of PaMprF H566C in nanodisc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MprF dimer

EntireName: MprF dimer
Components
  • Complex: MprF dimer
    • Protein or peptide: Phosphatidylglycerol lysyltransferase
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

-
Supramolecule #1: MprF dimer

SupramoleculeName: MprF dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Location in cell: Cell Membrane
Molecular weightTheoretical: 180 KDa

-
Macromolecule #1: Phosphatidylglycerol lysyltransferase

MacromoleculeName: Phosphatidylglycerol lysyltransferase / type: protein_or_peptide / ID: 1
Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 - Additional residues, 900-903 - VDAL - (N terminus of CPD), 1-32, 716-722, 805-833, 871-881 - Not modelled ...Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 - Additional residues, 900-903 - VDAL - (N terminus of CPD), 1-32, 716-722, 805-833, 871-881 - Not modelled in MprF. Residue H566 is mutated to cysteine, (numbering based on Uniprot and not the fusion construct)
Number of copies: 2 / Enantiomer: LEVO / EC number: lysyltransferase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 98.295445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSHPQFEKG GSGMRTDAPV PEHPAPPSSP ASPQRIRLID RITAYRQPIG LVFTLLLFGL ALVACYHLLR EIDPGALHDA IADVPRPAL LGALSATALG FVILLGYEWS ASRFAGVTLP MRSLATGGFS AFAIGNAVGL SLLSGGSVRY RLYSRHGIGA A EIARMTLF ...String:
MWSHPQFEKG GSGMRTDAPV PEHPAPPSSP ASPQRIRLID RITAYRQPIG LVFTLLLFGL ALVACYHLLR EIDPGALHDA IADVPRPAL LGALSATALG FVILLGYEWS ASRFAGVTLP MRSLATGGFS AFAIGNAVGL SLLSGGSVRY RLYSRHGIGA A EIARMTLF ASLSLGCALP VLAALAALCD LDDAASALHL PRALVAVIAI AVLSLAVGLV AFLARHRLPG ERPSPDSLLV RL GRRSLRL PGLRLSLLQL LITALDVAAA ATVLYLLLPE TPPFAAFLLV YLLALAAGVL SHVPGGVGVF EAVLLAAFAG QLG AAPLAA ALLLYRLIYV VLPLLLACLL LLFLEARRLW VTRQAIRVAS GFAAPILAIL VFLSGVVLLF SGATPAIDTR LEHL GFLIP HRLIDASHLV ASLIGVLCLL LAQGLRRRLS AAWALTLVLL LVGALLSLLK GFDWEEASLL SLTAALLAMF RRSFY RPSR LMEVPFSPLY VGASICVVGA SVWLLLFANQ DVHYSNQLWW QFALDADAPR ALRAALGSCL LLLALALGWL LRAAPP AIR EPNAEELQRA ARIIRCSDQP DGGLALTGDK ALLFHESDDA FLMYARRGRS MIALYDPIGP AMQRAELIWQ FRDLCDL HH ARPVFYQVRA ENLPFYMDIG LTALKLGEEA RVDLLRFDLE NKGKEMKDLR YTWNRGQRDG LALEFHEPGQ APLDELKA I SDAWLGGKQV REKGFSLGRF TPAYLNFFRI AIVRHQGKPV AFANLLETDS RELASLDLMR VHPDAPKLTM EFLMLGLIL HYKAQGHARF SLGMVPLAGL QPRRGAPLTQ RLGALVFRRG EQFYNFQGLR RFKDKFQPDW EPRYLAVPAG LDPLVALADT AALIAGGLT GLVKRRNSSS VDAL

UniProtKB: Phosphatidylglycerol lysyltransferase

-
Macromolecule #2: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 2 / Number of copies: 2 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
200.0 mMNaClSodium Chloride
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
Details: Glow discharge was performed at 25 mA with PELCO easyglow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3180 / Average exposure time: 60.0 sec. / Average electron dose: 30.4 e/Å2
Details: Images were collected in movie-mode at 40 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130481 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1434841
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.14), RELION (ver. 4), cryoSPARC (ver. 4.5.3))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated from the data using Relion and Cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 131805
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.36)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

0528


Chain - Chain ID: A / Chain - Residue range: 33-870 / Chain - Source name: Other / Chain - Initial model type: experimental model
Details: The model from ND was rigid body fit and manually adjusted for H566C ND map
RefinementProtocol: OTHER / Overall B value: 143.4
Output model

PDB-9w51:
MprF from Pseudomonas aeruginosa mutant, H566C in nanodisc, C2 symmetry

+
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