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- PDB-9ltt: Cryo-EM structure of Rhizobium etli MprF complexed with Lys-N-tRN... -

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Basic information

Entry
Database: PDB / ID: 9ltt
TitleCryo-EM structure of Rhizobium etli MprF complexed with Lys-N-tRNA(Lys)
Components
  • Hypothetical conserved protein
  • Lys-N-tRNA(Lys)
KeywordsMEMBRANE PROTEIN / Flippase / Aminoacyl-tRNA / Phosphatidylglycerol / Complex
Function / homology
Function and homology information


aminoacyltransferase activity / phospholipid homeostasis / plasma membrane
Similarity search - Function
: / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
LYSINE / Chem-PGW / : / RNA / RNA (> 10) / Hypothetical conserved protein
Similarity search - Component
Biological speciesRhizobium etli CFN 42 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsNishimura, M. / Hirano, H. / Gill, C.P. / Phan, C.N.K. / Gamper, H.B. / Will, A. / Yamashita, K. / Yashiro, Y. / Kobayashi, K. / Kise, Y. ...Nishimura, M. / Hirano, H. / Gill, C.P. / Phan, C.N.K. / Gamper, H.B. / Will, A. / Yamashita, K. / Yashiro, Y. / Kobayashi, K. / Kise, Y. / Kusakizako, T. / Itoh, Y. / Tomita, K. / Hou, Y.M. / Nishizawa, T. / Roy, H. / Nureki, O.
Funding support Japan, United States, 6items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E2 Japan
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI144481-02 United States
Japan Society for the Promotion of Science (JSPS)20H03216 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM134931 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI139202 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI164490 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Rhizobium etli MprF complexed with Lys-N-tRNA(Lys)
Authors: Nishimura, M.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical conserved protein
B: Hypothetical conserved protein
C: Lys-N-tRNA(Lys)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,6039
Polymers211,3133
Non-polymers3,2906
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1), (-1), (1)193.224, 193.224

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Components

#1: Protein Hypothetical conserved protein


Mass: 93918.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence refers to NCBI Protein database (IPG: 15109202)
Source: (gene. exp.) Rhizobium etli CFN 42 (bacteria) / Gene: RHE_CH03486 / Plasmid: pTSP1 / Details (production host): pET-modified vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2K4J4
#2: RNA chain Lys-N-tRNA(Lys)


Mass: 23475.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rhizobium etli CFN 42 (bacteria) / References: GenBank: 1190239608
#3: Chemical
ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: MprF complexed with Lys-N-tRNA / Type: COMPLEX / Entity ID: #2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.212 MDa / Experimental value: NO
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTSP1
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H11NO3-HCl1
2150 mMsodium chlorideNaCl1
30.06 %GDNC56H92O251
4100 uMTCEPC9H15O6P1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: a waiting time of 10 s and a blotting time of 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 2.6 sec. / Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 17101
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4cryoSPARC4CTF correction
7Cootmodel fitting
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11cryoSPARC4classification
12cryoSPARC43D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76710 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17F47

7f47

17F471PDBexperimental model
21EHZ

1ehz

11EHZ2PDBexperimental model

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