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Yorodumi- EMDB-41062: CryoEM structure of an inward-facing MelBSt at a Na(+)-bound and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41062 | |||||||||
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Title | CryoEM structure of an inward-facing MelBSt at a Na(+)-bound and sugar low-affinity conformation | |||||||||
Map data | The model was refined against this map. | |||||||||
Sample |
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Keywords | Sugar transporter / Cation-coupled symporter / Na(+) binding / Protein conformation / Nanobodies / NabFab / CryoEM / Membrane proteins / protein-protein interaction / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information organic substance transport / symporter activity / sodium ion transport / carbohydrate transport / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Guan L | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2024 Title: Mobile barrier mechanisms for Na-coupled symport in an MFS sugar transporter. Authors: Parameswaran Hariharan / Yuqi Shi / Satoshi Katsube / Katleen Willibal / Nathan D Burrows / Patrick Mitchell / Amirhossein Bakhtiiari / Samantha Stanfield / Els Pardon / H Ronald Kaback / ...Authors: Parameswaran Hariharan / Yuqi Shi / Satoshi Katsube / Katleen Willibal / Nathan D Burrows / Patrick Mitchell / Amirhossein Bakhtiiari / Samantha Stanfield / Els Pardon / H Ronald Kaback / Ruibin Liang / Jan Steyaert / Rosa Viner / Lan Guan / Abstract: While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial ...While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport. #1: Journal: Elife / Year: 2024 Title: Mobile barrier mechanisms for Na+-coupled symport in an MFS sugar transporter Authors: Hariharan P / Shi Y / Katsube S / Willibal K / Burrows ND / Mitchell P / Bakhtiiari A / Stanfield S / Pardon E / Kaback HR / Liang R / Steyaert J / Viner R / Gran L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41062.map.gz | 198.3 MB | EMDB map data format | |
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Header (meta data) | emd-41062-v30.xml emd-41062.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41062_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_41062.png | 92.3 KB | ||
Masks | emd_41062_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-41062.cif.gz | 7.4 KB | ||
Others | emd_41062_additional_1.map.gz emd_41062_half_map_1.map.gz emd_41062_half_map_2.map.gz | 107.5 MB 200.5 MB 200.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41062 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41062 | HTTPS FTP |
-Related structure data
Related structure data | 8t60MC 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_41062.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The model was refined against this map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41062_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_41062_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41062_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41062_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MelBSt bound with Nb725_4-NabFab complex
Entire | Name: MelBSt bound with Nb725_4-NabFab complex |
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Components |
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-Supramolecule #1: MelBSt bound with Nb725_4-NabFab complex
Supramolecule | Name: MelBSt bound with Nb725_4-NabFab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 120 KDa |
-Macromolecule #1: Melibiose permease
Macromolecule | Name: Melibiose permease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 |
Molecular weight | Theoretical: 54.104438 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SISMTTKLSY GFGAFGKDFA IGIVYMYLMY YYTDVVGLSV GLVGTLFLVA RIWDAINDPI MGWIVNATRS RWGKFKPWIL IGTLTNSLV LFLLFSAHLF EGTAQVVFVC VTYILWGMTY TIMDIPFWSL VPTITLDKRE REQLVPFPRF FASLAGFVTA G ITLPFVSY ...String: SISMTTKLSY GFGAFGKDFA IGIVYMYLMY YYTDVVGLSV GLVGTLFLVA RIWDAINDPI MGWIVNATRS RWGKFKPWIL IGTLTNSLV LFLLFSAHLF EGTAQVVFVC VTYILWGMTY TIMDIPFWSL VPTITLDKRE REQLVPFPRF FASLAGFVTA G ITLPFVSY VGGADRGFGF QMFTLVLIAF FIASTIVTLR NVHEVYSSDN GVTAGRPHLT LKTIVGLIYK NDQLSCLLGM AL AYNIASN IINGFAIYYF TYVIGDADLF PYYLSYAGAA NLLTLIVFPR LVKMLSRRIL WAGASVMPVL SCAGLFAMAL ADI HNAALI VAAGIFLNIG TALFWVLQVI MVADTVDYGE FKLNIRCESI AYSVQTMVVK GGSAFAAFFI ALVLGLIGYT PNVA QSAQT LQGMQFIMIV LPVLFFMMTL VLYFRYYRLN GDMLRKIQIH LLDKYRKTPP FVEQPDSPAI SVVATSDVKA HHHHH HHHH H UniProtKB: Melibiose permease |
-Macromolecule #2: Nb725_4
Macromolecule | Name: Nb725_4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.817506 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSQRQLVESG GGLVQPGGSL RLSCAVSGII FRDNAMGWYR QAPGKEREWV ATITDLGYTA YADSVKGRFT ISRDNAKDTV YLQMNSLEP EDTAVYYCHL PGTAAGDYWG KGTPVTVSSL EVLFQGPHHH HHHHH |
-Macromolecule #3: NabFab_H Chain
Macromolecule | Name: NabFab_H Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 25.684463 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSYYSIHWV RQAPGKGLEW VAYISSSSSY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARGYQYWQYH ASWYWNGGLD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSYYSIHWV RQAPGKGLEW VAYISSSSSY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARGYQYWQYH ASWYWNGGLD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTH T |
-Macromolecule #4: NabFab_L Chain
Macromolecule | Name: NabFab_L Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 23.258783 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #5: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 5 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI CETA (4k x 4k) / Number real images: 20778 / Average exposure time: 0.0535 sec. / Average electron dose: 1.28 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: AB INITIO MODEL | ||||||||||
Output model | PDB-8t60: |