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- EMDB-63384: Cryo-EM map of Rhizobium etli MprF complexed with Lys-N-tRNA(Lys)... -

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Basic information

Entry
Database: EMDB / ID: EMD-63384
TitleCryo-EM map of Rhizobium etli MprF complexed with Lys-N-tRNA(Lys) with the improved density of the anticodon stem loop of Lys-N-tRNA(Lys)
Map data
Sample
  • Organelle or cellular component: MprF complexed with Lys-N-tRNA
KeywordsFlippase / Aminoacyl-tRNA / Phosphatidylglycerol / Complex / MEMBRANE PROTEIN
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 / Kobayashi K / Kise Y / Kusakizako T ...Nishimura M / Hirano H / Gill CP / Phan CNK / Gamper HB / Will A / Yamashita K / Kobayashi K / Kise Y / Kusakizako T / Itoh Y / Hou YM / Nishizawa T / Roy H / Nureki O
Funding support United States, Japan, 6 items
OrganizationGrant numberCountry
Other governmentJPMJCR20E2
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_63384.png

Downloads & links

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Map

FileDownload / File: emd_63384.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.394
Minimum - Maximum-1.212652 - 1.9646665
Average (Standard dev.)0.010371296 (±0.07855893)
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_63384_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63384_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63384_half_map_2.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 complexed with Lys-N-tRNA

EntireName: MprF complexed with Lys-N-tRNA
Components
  • Organelle or cellular component: MprF complexed with Lys-N-tRNA

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

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

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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

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