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Yorodumi- EMDB-23751: Outward facing conformation of the MetNI methionine ABC transport... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23751 | |||||||||
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Title | Outward facing conformation of the MetNI methionine ABC transporter in complex with lipo-MetQ | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information D-methionine transmembrane transport / methionine transport / amino acid transport / ATPase-coupled transmembrane transporter activity / transmembrane transport / membrane => GO:0016020 / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) / Neisseria meningitidis serogroup B (strain MC58) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.4 Å | |||||||||
Authors | Sharaf NG / Rees DC | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2021 Title: Characterization of the ABC methionine transporter from reveals that lipidated MetQ is required for interaction. Authors: Naima G Sharaf / Mona Shahgholi / Esther Kim / Jeffrey Y Lai / David G VanderVelde / Allen T Lee / Douglas C Rees / Abstract: NmMetQ is a substrate-binding protein (SBP) from that has been identified as a surface-exposed candidate antigen for meningococcal vaccines. However, this location for NmMetQ challenges the ...NmMetQ is a substrate-binding protein (SBP) from that has been identified as a surface-exposed candidate antigen for meningococcal vaccines. However, this location for NmMetQ challenges the prevailing view that SBPs in Gram-negative bacteria are localized to the periplasmic space to promote interaction with their cognate ABC transporter embedded in the bacterial inner membrane. To elucidate the roles of NmMetQ, we characterized NmMetQ with and without its cognate ABC transporter (NmMetNI). Here, we show that NmMetQ is a lipoprotein (lipo-NmMetQ) that binds multiple methionine analogs and stimulates the ATPase activity of NmMetNI. Using single-particle electron cryo-microscopy, we determined the structures of NmMetNI in the presence and absence of lipo-NmMetQ. Based on our data, we propose that NmMetQ tethers to membranes via a lipid anchor and has dual function and localization, playing a role in NmMetNI-mediated transport at the inner membrane and moonlighting on the bacterial surface. | |||||||||
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_23751.map.gz | 229.7 MB | EMDB map data format | |
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Header (meta data) | emd-23751-v30.xml emd-23751.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23751_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_23751.png | 29.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23751 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23751 | HTTPS FTP |
-Related structure data
Related structure data | 7mbzMC 7mc0C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23751.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.856 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ABC transporter, permease protein, Lipoprotein, ABC transporter, ...
Entire | Name: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding proteinATP-binding cassette transporter |
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Components |
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-Supramolecule #1: ABC transporter, permease protein, Lipoprotein, ABC transporter, ...
Supramolecule | Name: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding protein type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Neisseria meningitidis serogroup B (bacteria) / Strain: strain MC58 |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: C43 |
-Macromolecule #1: ABC transporter, permease protein
Macromolecule | Name: ABC transporter, permease protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Neisseria meningitidis serogroup B (strain MC58) (bacteria) Strain: MC58 |
Molecular weight | Theoretical: 24.363064 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MADLTFQQAV STIVGMKDEI FRALGETFVM VGLSTTFAVI FGTLLGVLLF VTSSRQLHYN KLVNFLLDNL VNLMRAFPFV ILMIAMIPA TRAIVGSTIG PVAASLVLSV SGLFYFARLV EQNLREVPKG VIEAAAAMGA PPIAIVCKVL LNEARAGMVS S ITVLAIGL ...String: MADLTFQQAV STIVGMKDEI FRALGETFVM VGLSTTFAVI FGTLLGVLLF VTSSRQLHYN KLVNFLLDNL VNLMRAFPFV ILMIAMIPA TRAIVGSTIG PVAASLVLSV SGLFYFARLV EQNLREVPKG VIEAAAAMGA PPIAIVCKVL LNEARAGMVS S ITVLAIGL LSYSAAAGMI GGGGLGDLAI RYGYYRYQTE VIIFIVALLV LLVILIQSTG NALARKLDKR |
-Macromolecule #2: Lipoprotein
Macromolecule | Name: Lipoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Neisseria meningitidis serogroup B (strain MC58) (bacteria) Strain: MC58 |
Molecular weight | Theoretical: 33.010246 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTFFKTLSA AALALILAAC GGQKDSAPAA SASAAADNGA AKKEIVFGTT VGDFGDMVKE QIQAELEKKG YTVKLVEFTD YVRPNLALA EGELDINVFQ HKPYLDDFKK EHNLDITEVF QVPTAPLGLY PGKLKSLEEV KDGSTVSAPN DPSNFARVLV M LDELGWIK ...String: MKTFFKTLSA AALALILAAC GGQKDSAPAA SASAAADNGA AKKEIVFGTT VGDFGDMVKE QIQAELEKKG YTVKLVEFTD YVRPNLALA EGELDINVFQ HKPYLDDFKK EHNLDITEVF QVPTAPLGLY PGKLKSLEEV KDGSTVSAPN DPSNFARVLV M LDELGWIK LKDGINPLTA SKADIAENLK NIKIVELEAA QLPRSRADVD FAVVNGNYAI SSGMKLTEAL FQEPSFAYVN WS AVKTADK DSQWLKDVTE AYNSDAFKAY AHKRFEGYKS PAAWNEGAAK KLEHHHHHHH HHH |
-Macromolecule #3: ABC transporter, ATP-binding protein
Macromolecule | Name: ABC transporter, ATP-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Neisseria meningitidis serogroup B (strain MC58) (bacteria) Strain: MC58 |
Molecular weight | Theoretical: 29.866152 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHHHHHHHH HHSSGHIDDD DKHMIILDKV SKHYQTRDKT RFAAVEPTSL EIRDGEIFGL MGYSGAGKST LLRLINLLER PDSGKVNVC GQELTALDAA ALRQARQNIG MVFQQFNLLS NRTVADNVAF PLEIAGWPSE KIKARVKECL EIVGLTERAG H YPAQLSGG ...String: MGHHHHHHHH HHSSGHIDDD DKHMIILDKV SKHYQTRDKT RFAAVEPTSL EIRDGEIFGL MGYSGAGKST LLRLINLLER PDSGKVNVC GQELTALDAA ALRQARQNIG MVFQQFNLLS NRTVADNVAF PLEIAGWPSE KIKARVKECL EIVGLTERAG H YPAQLSGG QKQRVGIARA LAPKPQVILA DEPTSALDPA TTRSVLECLE DINKRFNVTI VIVTHEMSVI RRLCDRAALL DK GKVVEIV EVRGNQIHAQ SDIGRELIRE D |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 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 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
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Output model | PDB-7mbz: |