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Open data
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Basic information
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Title | Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position T68C | ||||||||||||
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Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
![]() | 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 | ![]()
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![]() | ![]() 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 | ![]() | 18.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.6 KB 23.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.2 KB | Display | ![]() |
Images | ![]() | 84.8 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 6.3 MB 18.6 MB 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 680.9 KB | Display | ![]() |
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Full document | ![]() | 680.5 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ph7MC ![]() 7ndfC ![]() 7ph2C ![]() 7ph3C ![]() 7ph4C 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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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
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
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-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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-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 | ||||||||||||
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-Half map: #2
File | emd_13409_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
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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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 65.760852 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 12.339852 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.6 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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |