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- EMDB-63380: Cryo-EM structure of Rhizobium etli MprF complexed with Lys-N-tRN... -

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Basic information

Entry
Database: EMDB / ID: EMD-63380
TitleCryo-EM structure of Rhizobium etli MprF complexed with Lys-N-tRNA(Lys)
Map data
Sample
  • Complex: MprF complexed with Lys-N-tRNA
    • RNA: Lys-N-tRNA(Lys)
  • Protein or peptide: Hypothetical conserved protein
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: LYSINE
KeywordsFlippase / Aminoacyl-tRNA / Phosphatidylglycerol / Complex / MEMBRANE PROTEIN
Function / homology: / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / aminoacyltransferase activity / phospholipid homeostasis / Acyl-CoA N-acyltransferase / plasma membrane / Hypothetical conserved protein
Function and homology information
Biological speciesRhizobium etli CFN 42 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsNishimura M / Hirano H / Gill CP / Phan CNK / Gamper HB / Will A / Yamashita K / Yashiro Y / Kobayashi K / Kise Y ...Nishimura M / Hirano H / Gill CP / Phan CNK / Gamper HB / Will A / Yamashita K / Yashiro Y / Kobayashi K / Kise Y / Kusakizako T / Itoh Y / Tomita K / Hou YM / Nishizawa T / Roy H / Nureki O
Funding support Japan, United States, 6 items
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, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63380.png

Downloads & links

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Map

FileDownload / File: emd_63380.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 200 pix.
= 200.11 Å		1 Å/pix.
x 200 pix.
= 200.11 Å		1 Å/pix.
x 200 pix.
= 200.11 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-1.3000879 - 1.9786973
Average (Standard dev.)0.01031078 (±0.08977227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 200.10957 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63380_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63380_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63380_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MprF complexed with Lys-N-tRNA

EntireName: MprF complexed with Lys-N-tRNA
Components
  • Complex: MprF complexed with Lys-N-tRNA
    • RNA: Lys-N-tRNA(Lys)
  • Protein or peptide: Hypothetical conserved protein
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: LYSINE

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Supramolecule #1: MprF complexed with Lys-N-tRNA

SupramoleculeName: MprF complexed with Lys-N-tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Molecular weightTheoretical: 212 KDa

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Macromolecule #1: Hypothetical conserved protein

MacromoleculeName: Hypothetical conserved protein / type: protein_or_peptide / ID: 1
Details: Sequence refers to NCBI Protein database (IPG: 15109202)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Molecular weightTheoretical: 93.918508 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSGHGNLEEM EATDGFSFRT LFRRYRTPLT AAATLIVFCL VGYAIMQLTN EVRYDDVVAA LAATGPSAIL LALFFTALSF LSLVFYDLN AIEYIGKKLP FPHVALTAFS AYAVGNTAGF GALSGGAIRY RAYTRLGLSP EDIGRIIAFV TLSFGLGLAA V ASIALIII ...String:
MSGHGNLEEM EATDGFSFRT LFRRYRTPLT AAATLIVFCL VGYAIMQLTN EVRYDDVVAA LAATGPSAIL LALFFTALSF LSLVFYDLN AIEYIGKKLP FPHVALTAFS AYAVGNTAGF GALSGGAIRY RAYTRLGLSP EDIGRIIAFV TLSFGLGLAA V ASIALIII ASEIGPLIGV SPFLLRLIAG SIIAILGAVM IIGREGRVLN FGAVAIRLPD SRTWSRQFLV TAFDIAASAS VL YVLLPQT AIGWPVFLAV YAIAVGLGVL SHVPAGLGVF ETVIIASLGS AVNIDAVLGS LVLYRLIYHV LPLLIAVLAV SAA ELRRFV DHPAASSVRR IGGRLMPQLL STLALLLGVM LVFSSVTPTP DQNLEFLSNY LPLPMVEGAH FLSSLLGLAL VVAA RGLGQ RLDGAWWVAV FSAVAALTLS LLKAIALVEA AFLAFLIFGL FVSRRLFTRH ASLLNQAMTA SWLMAIAVIV VGAVV ILLF VYRDVEYSNE LWWQFEFTAE APRGLRALLG ITIISSAIAI FSLLRPATFR PEPATEEALT RAVEIVRKQG NADANL VRM GDKSIMFSEK GDAFIMYGRQ GRSWIALFDP VGDHGAVQEL VWRFVEAARA AGCRAVFYQI SPALLSHCAD AGLRAFK LG ELAVADLRTF EMKGGKWANL RQTASRAQRD GLEFAVVEPE NVPDIIDELA AVSTAWLEHH NAKEKGFSLG SFDPDYVS A QPVGILKKDG KIVAFANILV TESKEEGTID LMRFSPDAPK GSMDFLFVQI MEYLRNQGFT HFNLGMAPLS GMSKREAAP VWDRIGSTVF EHGERFYNFK GLRAFKSKFH PHWQPRYLAV SGGGNPMIAL MDATFLIGGG LKGVVRK

UniProtKB: Hypothetical conserved protein

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Macromolecule #2: Lys-N-tRNA(Lys)

MacromoleculeName: Lys-N-tRNA(Lys) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Molecular weightTheoretical: 23.475914 KDa
SequenceString:
GGGUGAUUAG CUCAGUUGGU AGAGCAGCUG ACUCUUAAUC AGCGGGUCGU AGGUUCGAGC CCUACAUCAC CCA

GENBANK: GENBANK: CP020906.1

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Macromolecule #3: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 3 / Number of copies: 4 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #4: LYSINE

MacromoleculeName: LYSINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: LYS
Molecular weightTheoretical: 147.195 Da
Chemical component information

ChemComp-LYS:
LYSINE

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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

Concentration3.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3-HClTris-HCl
150.0 mMNaClsodium chloride
0.06 %C56H92O25GDN
100.0 uMC9H15O6PTCEP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: a waiting time of 10 s and a blotting time of 4 s.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 17101 / Average exposure time: 2.6 sec. / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 76710
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7f47

source_name: PDB, initial_model_type: experimental model

1ehz

source_name: PDB, initial_model_type: experimental model
RefinementSpace: RECIPROCAL
Output model

PDB-9ltt:
Cryo-EM structure of Rhizobium etli MprF complexed with Lys-N-tRNA(Lys)

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