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- EMDB-61238: MprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-61238
TitleMprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry
Map dataSharpened Full Map
Sample
  • Complex: MprF dimer
    • Protein or peptide: Phosphatidylglycerol lysyltransferase
  • Ligand: (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsMultiple peptide resistance factor / Membrane Enzyme / Synthase / Flippase / aminoacylated lipid / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJha S / Vinothkumar KR
Funding support India, 2 items
OrganizationGrant numberCountry
Other governmentDepartment of Atomic Energy, Government of India, RTI 4006
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Structures of Multiple Peptide Resistance Factor from Pseudomonas aeruginosa
Authors: Jha S / Vinothkumar KR
History
DepositionAug 21, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61238.png

Downloads & links

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Map

FileDownload / File: emd_61238.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Full Map
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: 0.57
Minimum - Maximum-7.9576826 - 9.483133
Average (Standard dev.)0.00028835778 (±0.15259267)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: Unsharpened Half Map

Fileemd_61238_half_map_1.map
AnnotationUnsharpened Half Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened Half Map

Fileemd_61238_half_map_2.map
AnnotationUnsharpened Half Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MprF dimer

EntireName: MprF dimer
Components
  • Complex: MprF dimer
    • Protein or peptide: Phosphatidylglycerol lysyltransferase
  • Ligand: (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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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

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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 (RNSSS) - additional residues, from fusion protein 900-903 - VDAL - (N terminus of CPD after cleavage), 1-32, ...Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 (RNSSS) - additional residues, from fusion protein 900-903 - VDAL - (N terminus of CPD after cleavage), 1-32, 713-726, 805-832, 873-881 - Not modelled (numbering based on Uniprot and doesn't include the fusion construct)
Number of copies: 2 / Enantiomer: LEVO / EC number: lysyltransferase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1
Molecular weightTheoretical: 98.330453 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 ARIIRHSDQP 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

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Macromolecule #2: (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S}...

MacromoleculeName: (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R}) ...Name: (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol
type: ligand / ID: 2 / Number of copies: 2 / Formula: J4U
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-J4U:
(2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol

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Macromolecule #3: (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: 3 / Number of copies: 22 / 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

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Macromolecule #4: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 4 / Number of copies: 12 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / 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

Concentration5.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
200.0 mMNaClSodium Chloride
5.0 mMC2H6OS2-mercaptoethanol
0.006 %C56H92O25GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: The grid was glow discharged at 25 mA with PELCO easyglow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force, 0.

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Electron microscopy

MicroscopeFEI TITAN 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: 2 / Number real images: 3877 / Average exposure time: 60.0 sec. / Average electron dose: 28.75 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: 13084 / 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

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Image processing

Particle selectionNumber selected: 1239668
CTF correctionSoftware: (Name: Gctf (ver. 1.06), RELION (ver. 4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Using SGD within Relion
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 109157
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

4v35

residue_range: 574-872, source_name: PDB, initial_model_type: experimental modelridid body docked and manually adjusted using coot
residue_range: 33-573, source_name: Other, initial_model_type: in silico modelThe initial model was built as polyalanine helices followed by sequence assignment
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 146.5
Output model

PDB-9j8q:
MprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry

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