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Yorodumi- EMDB-13985: Cryo-EM map of apo-EleNRMT in complex with two nanobodies at 3.5A -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13985 | |||||||||
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Title | Cryo-EM map of apo-EleNRMT in complex with two nanobodies at 3.5A | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | NRAMP family / Natural resistance-associated macrophage protein-like / metal ion transmembrane transporter activity / membrane / Divalent metal cation transporter Function and homology information | |||||||||
Biological species | Eggerthella lenta (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ramanadane K / Straub MS / Dutzler R / Manatschal C | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Elife / Year: 2022 Title: Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family. Authors: Karthik Ramanadane / Monique S Straub / Raimund Dutzler / Cristina Manatschal / Abstract: Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca and ...Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca and Mg, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg. The protein transports Mg and Mn but not Ca by a mechanism that is not coupled to H. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13985.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-13985-v30.xml emd-13985.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13985_fsc.xml | 8.3 KB | Display | FSC data file |
Images | emd_13985.png | 135.8 KB | ||
Masks | emd_13985_msk_1.map | 22.2 MB | Mask map | |
Others | emd_13985_half_map_1.map.gz emd_13985_half_map_2.map.gz | 20.7 MB 20.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13985 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13985 | HTTPS FTP |
-Related structure data
Related structure data | 7qiaMC 7qicC 7qjiC 7qjjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13985.map.gz / Format: CCP4 / Size: 22.2 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: 1.302 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13985_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13985_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13985_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : EleNRMT in complex with two nanobodies
Entire | Name: EleNRMT in complex with two nanobodies |
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Components |
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-Supramolecule #1: EleNRMT in complex with two nanobodies
Supramolecule | Name: EleNRMT in complex with two nanobodies / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 0.013 kDa/nm |
-Supramolecule #2: EleNRMT
Supramolecule | Name: EleNRMT / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: thermostabilized version |
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Source (natural) | Organism: Eggerthella lenta (bacteria) |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
-Supramolecule #3: Nanobody 1
Supramolecule | Name: Nanobody 1 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
-Supramolecule #4: Nanobody 2
Supramolecule | Name: Nanobody 2 / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
-Macromolecule #1: Divalent metal cation transporter
Macromolecule | Name: Divalent metal cation transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Eggerthella lenta (bacteria) |
Molecular weight | Theoretical: 46.848828 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: MMMKKNEKLE LRDVAVDAAE STELVEVPEK KQPKKIWLLL AALGPGIVTA MAGNDAGGIS TYSTVGAKFG FATLWVIPIM CVLLIVVQM TAARMGAVTG KGFAALIRER FGIRLTALAM LALLIGNVAT TFSEFAGIAS GMEMFGVSKY LSVPVAAVAV W LLVVGGSY ...String: MMMKKNEKLE LRDVAVDAAE STELVEVPEK KQPKKIWLLL AALGPGIVTA MAGNDAGGIS TYSTVGAKFG FATLWVIPIM CVLLIVVQM TAARMGAVTG KGFAALIRER FGIRLTALAM LALLIGNVAT TFSEFAGIAS GMEMFGVSKY LSVPVAAVAV W LLVVGGSY KRVEKVFLIL SLVFVTYIVA AFMAQPNWEE ALTSTVVPHI VNDQSFVSLV IAMIGTTIAP WMMFFNQSNV VE KGVTVKD LFSQKVDVVA GTIAACLVAW FIIVTTGAVL FPQGIEIESA ADAARALAPF AGHYAEALFA IGLIAASFLA ACV LPLTTA FVICEAFGWE AGVSFKWKEA PLFKSIFTFV IAFSAVVVLI PNIDLMGVML TAQFVNGLIL PVLLVFMAII AADK RVMGA YRSRIVSRVL IWLTVGIVTV LTAALLVMQV LGI |
-Macromolecule #2: Nanobody 1
Macromolecule | Name: Nanobody 1 / 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: 13.12676 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: QLQLVESGGG LVQPGGSLRL SCEASGKVFM INAMGWYRQA PGKQRELVAF ISRRGNINYA DSVKGRFTIS RDNAKNTVYL QMNSLRPED TAIYYCSADP RSNLDDGRYW GKGTPVTVSS |
-Macromolecule #3: Nanobody 2
Macromolecule | Name: Nanobody 2 / 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: 13.767339 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: QLQLVESGGG LVLAGGSLRL SCAASVRTFS HYALGWFRQA PGKEREFVAA IRWTGSSANY ADSVKGRFTI SRDNAKNTVD LRMNSLKPE DTAVYYCAAR TVYRPGFEDP NEYAYWGQGT RVTVSS |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 3 / 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 | 3.5 mg/mL | ||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-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: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 22117 / Average exposure time: 1.01 sec. / Average electron dose: 69.725 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |