+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13409 | ||||||||||||
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Title | Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position T68C | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / Vicugna pacos (alpaca) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Januliene D / Parey K / Galazzo L / Meier G / Vecchis D / Striednig B / Hilbi H / Schaefer LV / Kuprov I / Bordignon E ...Januliene D / Parey K / Galazzo L / Meier G / Vecchis D / Striednig B / Hilbi H / Schaefer LV / Kuprov I / Bordignon E / Seeger MA / Moeller A | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Sci Adv / Year: 2022 Title: The ABC transporter MsbA adopts the wide inward-open conformation in cells. Authors: Laura Galazzo / Gianmarco Meier / Dovile Januliene / Kristian Parey / Dario De Vecchis / Bianca Striednig / Hubert Hilbi / Lars V Schäfer / Ilya Kuprov / Arne Moeller / Enrica Bordignon / Markus A Seeger / Abstract: Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their ...Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13409.map.gz | 18.6 MB | EMDB map data format | |
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Header (meta data) | emd-13409-v30.xml emd-13409.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13409_fsc.xml | 11.2 KB | Display | FSC data file |
Images | emd_13409.png | 84.8 KB | ||
Masks | emd_13409_msk_1.map | 125 MB | Mask map | |
Others | emd_13409_additional_1.map.gz emd_13409_additional_2.map.gz emd_13409_half_map_1.map.gz emd_13409_half_map_2.map.gz | 6.3 MB 18.6 MB 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13409 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13409 | HTTPS FTP |
-Related structure data
Related structure data | 7ph7MC 7ndfC 7ph2C 7ph3C 7ph4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13409.map.gz / Format: CCP4 / Size: 19.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13409_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally filtered map, used for figures and assisted model building
File | emd_13409_additional_1.map | ||||||||||||
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Annotation | Locally filtered map, used for figures and assisted model building | ||||||||||||
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Density Histograms |
-Additional map: Density modified map, used for model building
File | emd_13409_additional_2.map | ||||||||||||
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Annotation | Density modified map, used for model building | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13409_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13409_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli MsbA in complex with nanobody Nb_MsbA#1, labeled with Gd-...
Entire | Name: E. coli MsbA in complex with nanobody Nb_MsbA#1, labeled with Gd-DOTA at T68C |
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Components |
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-Supramolecule #1: E. coli MsbA in complex with nanobody Nb_MsbA#1, labeled with Gd-...
Supramolecule | Name: E. coli MsbA in complex with nanobody Nb_MsbA#1, labeled with Gd-DOTA at T68C type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: ATP-binding transport protein multicopy suppressor of htrB
Macromolecule | Name: ATP-binding transport protein multicopy suppressor of htrB type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 65.760852 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPDEAEKLFN QMHNDKDLST WQTFRRLWPT IAPFKAGLIV AGVALILNAA SDTFMLSLLK PLLDDGFGKT DRSVLVWMPL VVIGLMILR GITSYVSSYC ISWVSGKVVM TMRRRLFGHM MGMPVSFFDK QSTGTLLSRI TYDSEQVASS SSGALITVVR E GASIIGLF ...String: GPDEAEKLFN QMHNDKDLST WQTFRRLWPT IAPFKAGLIV AGVALILNAA SDTFMLSLLK PLLDDGFGKT DRSVLVWMPL VVIGLMILR GITSYVSSYC ISWVSGKVVM TMRRRLFGHM MGMPVSFFDK QSTGTLLSRI TYDSEQVASS SSGALITVVR E GASIIGLF IMMFYYSWQL SIILIVLAPI VSIAIRVVSK RFRNISKNMQ NTMGQVTTSA EQMLKGHKEV LIFGGQEVET KR FDKVSNR MRLQGMKMVS ASSISDPIIQ LIASLALAFV LYAASFPSVM DSLTAGTITV VFSSMIALMR PLKSLTNVNA QFQ RGMAAC QTLFTILDSE QEKDEGKRVI ERATGDVEFR NVTFTYPGRD VPALRNINLK IPAGKTVALV GRSGSGKSTI ASLI TRFYD IDEGEILMDG HDLREYTLAS LRNQVALVSQ NVHLFNDTVA NNIAYARTEQ YSREQIEEAA RMAYAMDFIN KMDNG LDTV IGENGVLLSG GQRQRIAIAR ALLRDSPILI LDEATSALDT ESERAIQAAL DELQKNRTSL VIAHRLSTIE KADEIV VVE DGVIVERGTH NDLLEHRGVY AQLHKMQFGQ |
-Macromolecule #2: Nb_MsbA#1
Macromolecule | Name: Nb_MsbA#1 / type: protein_or_peptide / ID: 2 / Details: Nanobody is labeled with GMO-GD at Cys68 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 12.339852 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPSQMQLVES GGGLVQAGGS LRLSCAVSGS IFSIITLAWY RQAPGKPREN VATITRGSRT SYADSVKGRF CISKDNAKST VYLQMNKLK PEDTADYYCN AEGPAGYWGQ GTPVTVS |
-Macromolecule #3: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(...
Macromolecule | Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl) ...Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic acid type: ligand / ID: 3 / Number of copies: 1 / Formula: EIW |
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Molecular weight | Theoretical: 2.206503 KDa |
Chemical component information | ChemComp-EIW: |
-Macromolecule #4: (1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)p...
Macromolecule | Name: (1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione type: ligand / ID: 4 / Number of copies: 2 / Formula: 88T |
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Molecular weight | Theoretical: 524.524 Da |
Chemical component information | ChemComp-88T: |
-Macromolecule #5: GADOLINIUM ATOM
Macromolecule | Name: GADOLINIUM ATOM / type: ligand / ID: 5 / Number of copies: 2 / Formula: GD |
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Molecular weight | Theoretical: 157.25 Da |
Chemical component information | ChemComp-GD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.6 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |