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- EMDB-31445: Cryo-EM structure of Rhizobium etli MprF -

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Basic information

Entry
Database: EMDB / ID: EMD-31445
TitleCryo-EM structure of Rhizobium etli MprF
Map data3.0 A "Best map" by EMDA
Sample
  • Organelle or cellular component: MprF
    • 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: [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate
  • Ligand: water
Keywordsflippase / aminoacyl-tRNA / phosphatidylglycerol / 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) / Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsNishimura M / Hirano H
CitationJournal: To Be Published
Title: Cryo-EM structure of Rhizobium etli MprF
Authors: Nishimura M
History
DepositionJun 17, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31445.png

Downloads & links

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Map

FileDownload / File: emd_31445.map.gz / Format: CCP4 / Size: 27.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.0 A "Best map" by EMDA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 194 pix.
= 193.224 Å		1 Å/pix.
x 194 pix.
= 193.224 Å		1 Å/pix.
x 194 pix.
= 193.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000299
Minimum - Maximum-0.0021232832 - 0.0032375494
Average (Standard dev.)0.00000054811767 (±0.00010953165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions194194194
Spacing194194194
CellA=B=C: 193.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_31445_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31445_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31445_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : MprF

EntireName: MprF
Components
  • Organelle or cellular component: MprF
    • 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: [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate
  • Ligand: water

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Supramolecule #1: MprF

SupramoleculeName: MprF / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Molecular weightTheoretical: 187 KDa

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Macromolecule #1: Hypothetical conserved protein

MacromoleculeName: Hypothetical conserved protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhizobium etli (strain CFN 42 / ATCC 51251) (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: (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: 2 / Number of copies: 1 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #3: [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-pro...

MacromoleculeName: [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate
type: ligand / ID: 3 / Number of copies: 1 / Formula: 1K1
Molecular weightTheoretical: 877.179 Da
Chemical component information

ChemComp-1K1:
[(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3-HClTris-HCl
150.0 mMNaClsodium chloride
0.06 %C56H92O25GDN
100.0 uMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / 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

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
DetailsCDS mode
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3159 / Average exposure time: 5.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 307241
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5vrv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL
Output model

PDB-7f47:
Cryo-EM structure of Rhizobium etli MprF

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