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Open data
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Basic information
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Title | Cryo-EM structure of Rhizobium etli MprF | |||||||||
![]() | 3.0 A "Best map" by EMDA | |||||||||
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![]() | flippase / aminoacyl-tRNA / phosphatidylglycerol / MEMBRANE PROTEIN | |||||||||
Function / homology | Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase / membrane => GO:0016020 / plasma membrane / Hypothetical conserved protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
![]() | Nishimura M / Hirano H | |||||||||
![]() | ![]() Title: Cryo-EM structure of Rhizobium etli MprF Authors: Nishimura M | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 159 KB | ||
Masks | ![]() | 27.9 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 23.2 MB 23.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 724.3 KB | Display | ![]() |
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Full document | ![]() | 723.8 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f47MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3.0 A "Best map" by EMDA | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.996 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31445_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31445_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MprF
Entire | Name: MprF |
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Components |
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-Supramolecule #1: MprF
Supramolecule | Name: MprF / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 187 KDa |
-Macromolecule #1: Hypothetical conserved protein
Macromolecule | Name: Hypothetical conserved protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.918508 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...
Macromolecule | Name: (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 |
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Molecular weight | Theoretical: 749.007 Da |
-Macromolecule #3: [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-pro...
Macromolecule | Name: [(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 |
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Molecular weight | Theoretical: 877.179 Da |
Chemical component information | ![]() ChemComp-1K1: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: 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 | |||||||||||||||
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Details | CDS mode |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |