[English] 日本語
Yorodumi
- PDB-9j8r: MprF from Pseudomonas aeruginosa in GDN micelle, C1 symmetry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j8r
TitleMprF from Pseudomonas aeruginosa in GDN micelle, C1 symmetry
ComponentsPhosphatidylglycerol lysyltransferase
KeywordsMEMBRANE PROTEIN / Multiple peptide resistance factor / Membrane Enzyme / Synthase / Flippase / aminoacylated lipid
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
Chem-J4U / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / Phosphatidylglycerol lysyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJha, S. / Vinothkumar, K.R.
Funding support India, 2items
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: To Be Published
Title: Structures of Multiple Peptide Resistance Factor from Pseudomonas aeruginosa
Authors: Jha, S. / Vinothkumar, K.R.
History
DepositionAug 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylglycerol lysyltransferase
B: Phosphatidylglycerol lysyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,32338
Polymers196,6612
Non-polymers27,66236
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Phosphatidylglycerol lysyltransferase / Lysylphosphatidylglycerol synthase / phosphatidylglycerol alanyltransferase


Mass: 98330.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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)
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0920 / Plasmid: pET22b-CPD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I537, lysyltransferase
#2: Chemical 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


Mass: 1165.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H92O25
#3: Chemical...
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#4: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: MprF dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Cellular location: Cell membrane
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) C41 / Plasmid: pET22b-CPD
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2200 mMSodium ChlorideNaCl1
35 mM2-mercaptoethanolC2H6OS1
40.006 %GDNC56H92O251
SpecimenConc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grids were glow discharged at 25 mA using PELCO easyglow
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K / Details: Blot force, 0

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 130841 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 28.75 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3877
Details: Images were collected in movie-mode at 40 frames per second
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4Gctf1.06CTF correction
5RELION4CTF correction
8Coot0.9.8.8model fitting
9UCSF Chimera1.17.3model fitting
11PHENIX1.20.1-4487model refinement
12REFMAC5.8.0411model refinement
13RELION4initial Euler assignment
14cryoSPARC4.3final Euler assignment
15cryoSPARC4.3classification
16cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1239668
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109157 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 170.7 / Protocol: OTHER / Space: RECIPROCAL
Atomic model buildingAccession code: D_1300050528 / Details: complete dimer was used to dock in C1 map / Source name: Other / Type: experimental model
RefinementResolution: 3.4→154.08 Å / Cor.coef. Fo:Fc: 0.886 / SU B: 16.393 / SU ML: 0.27 / ESU R: 0.73
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.34339 --
obs0.34339 85667 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 168.413 Å2
Refinement stepCycle: 1 / Total: 13056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0020.01213314
ELECTRON MICROSCOPYr_bond_other_d00.01613868
ELECTRON MICROSCOPYr_angle_refined_deg0.6721.63517918
ELECTRON MICROSCOPYr_angle_other_deg0.2231.55231876
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.45651592
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.184.882136
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.6102016
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0350.22060
ELECTRON MICROSCOPYr_gen_planes_refined0.0020.0214786
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022982
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.19916.2166386
ELECTRON MICROSCOPYr_mcbond_other6.19916.2166386
ELECTRON MICROSCOPYr_mcangle_it10.60229.1527972
ELECTRON MICROSCOPYr_mcangle_other10.60129.1557973
ELECTRON MICROSCOPYr_scbond_it6.51617.6756928
ELECTRON MICROSCOPYr_scbond_other6.51517.6756929
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other11.79932.0439947
ELECTRON MICROSCOPYr_long_range_B_refined17.64314914202
ELECTRON MICROSCOPYr_long_range_B_other17.64314914203
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.297 6271 -
obs--100 %

+
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