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- EMDB-39773: Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ -
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Open data
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Basic information
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Title | Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ | |||||||||
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![]() | complex / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Qiao Z / Gao YG | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ. Authors: Qiao Z / Gao YG | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 57.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 94.2 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() | 48.3 MB 48.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8z5g M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.46 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_39773_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39773_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : QmcA-YbbJ complex
Entire | Name: QmcA-YbbJ complex |
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Components |
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-Supramolecule #1: QmcA-YbbJ complex
Supramolecule | Name: QmcA-YbbJ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Protein QmcA
Macromolecule | Name: Protein QmcA / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 33.778023 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLIFIPILIF VALVIVGAGV KIVPQGYQWT VERFGRYTKT LQPGLSLVVP FMDRIGRKIN MMEQVLDIPS QEVISKDNAN VTIDAVCFI QVIDAPRAAY EVSNLELAII NLTMTNIRTV LGSMELDEML SQRDSINSRL LRIVDEATNP WGIKVTRIEI R DVRPPAEL ...String: MLIFIPILIF VALVIVGAGV KIVPQGYQWT VERFGRYTKT LQPGLSLVVP FMDRIGRKIN MMEQVLDIPS QEVISKDNAN VTIDAVCFI QVIDAPRAAY EVSNLELAII NLTMTNIRTV LGSMELDEML SQRDSINSRL LRIVDEATNP WGIKVTRIEI R DVRPPAEL ISSMNAQMKA ERTKRAYILE AEGIRQAEIL KAEGEKQSQI LKAEGERQSA FLQAEARERS AEAEARATKM VS EAIASGD IQAVNYFVAQ KYTEALQQIG SSSNSKVVMM PLEASSLMGS IAGIAELVKD SANKRTQP UniProtKB: Protein QmcA |
-Macromolecule #2: Inner membrane protein YbbJ
Macromolecule | Name: Inner membrane protein YbbJ / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.956775 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MMELMVVHPH IFWLSLGGLL LAAEMLGGNG YLLWSGVAAV ITGLVVWLVP LGWEWQGVMF AILTLLAAWL WWKWLSRRVR EQKHSDSHL NQRGQQLIGR RFVLESPLVN GRGHMRVGDS SWPVSASEDL GAGTHVEVIA IEGITLHIRA VSS UniProtKB: Inner membrane protein YbbJ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36372 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |