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Yorodumi- EMDB-13406: AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-l... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13406 | ||||||||||||
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Title | AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position T68C | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information MsbA transporter complex / lipopolysaccharide floppase activity / lipid translocation / ABC-type lipid A-core oligosaccharide transporter / lipopolysaccharide transport / ATPase-coupled lipid transmembrane transporter activity / ABC-type xenobiotic transporter activity / lipid transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport ...MsbA transporter complex / lipopolysaccharide floppase activity / lipid translocation / ABC-type lipid A-core oligosaccharide transporter / lipopolysaccharide transport / ATPase-coupled lipid transmembrane transporter activity / ABC-type xenobiotic transporter activity / lipid transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / lipid binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Vicugna pacos (alpaca) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 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_13406.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-13406-v30.xml emd-13406.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13406_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_13406.png | 100 KB | ||
Masks | emd_13406_msk_1.map | 125 MB | Mask map | |
Others | emd_13406_additional_1.map.gz emd_13406_additional_2.map.gz emd_13406_half_map_1.map.gz emd_13406_half_map_2.map.gz | 4.9 MB 15.2 MB 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13406 | HTTPS FTP |
-Validation report
Summary document | emd_13406_validation.pdf.gz | 807.4 KB | Display | EMDB validaton report |
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Full document | emd_13406_full_validation.pdf.gz | 806.9 KB | Display | |
Data in XML | emd_13406_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_13406_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13406 | HTTPS FTP |
-Related structure data
Related structure data | 7ph4MC 7ndfC 7ph2C 7ph3C 7ph7C 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_13406.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_13406_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Locally filtered map, used for figures and assisted model building
File | emd_13406_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_13406_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_13406_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13406_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AMP-PNP bound E. coli MsbA in complex with nanobody Nb_MsbA#1, la...
Entire | Name: AMP-PNP bound 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: AMP-PNP bound E. coli MsbA in complex with nanobody Nb_MsbA#1, la...
Supramolecule | Name: AMP-PNP bound 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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-Macromolecule #1: ATP-dependent lipid A-core flippase
Macromolecule | Name: ATP-dependent lipid A-core flippase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: ABC-type lipid A-core oligosaccharide transporter |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
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: Nanobody Nb_MsbA#1
Macromolecule | Name: Nanobody Nb_MsbA#1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 12.41093 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPSQMQLVES GGGLVQAGGS LRLSCAVSGS IFSIITLAWY RQAPGKPREN VATITRGSRT SYADSVKGRF CISKDNAKST VYLQMNKLK PEDTADYYCN AEGPAGYWGQ GTPVTVSA |
-Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ChemComp-LMT: |
-Macromolecule #6: (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: 6 / Number of copies: 2 / Formula: 88T |
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Molecular weight | Theoretical: 524.524 Da |
Chemical component information | ChemComp-88T: |
-Macromolecule #7: GADOLINIUM ATOM
Macromolecule | Name: GADOLINIUM ATOM / type: ligand / ID: 7 / Number of copies: 2 / Formula: GD |
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Molecular weight | Theoretical: 157.25 Da |
Chemical component information | ChemComp-GD: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / 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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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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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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |