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- EMDB-23751: Outward facing conformation of the MetNI methionine ABC transport... -

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Basic information

Entry
Database: EMDB / ID: EMD-23751
TitleOutward facing conformation of the MetNI methionine ABC transporter in complex with lipo-MetQ
Map datasharpened map
Sample
  • Complex: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding protein
    • Protein or peptide: ABC transporter, permease protein
    • Protein or peptide: Lipoprotein
    • Protein or peptide: ABC transporter, ATP-binding protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


D-methionine transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Methionine import ATP-binding protein MetN, ATP-binding domain / Lipoprotein NlpA family / NlpA lipoprotein / : / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site ...: / Methionine import ATP-binding protein MetN, ATP-binding domain / Lipoprotein NlpA family / NlpA lipoprotein / : / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lipoprotein / ABC transporter, ATP-binding protein / ABC transporter, permease protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria) / Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsSharaf NG / Rees DC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionApr 1, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mbz
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23751.png

Downloads & links

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Map

FileDownload / File: emd_23751.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342.4 Å		0.86 Å/pix.
x 400 pix.
= 342.4 Å		0.86 Å/pix.
x 400 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.09729297 - 0.27828625
Average (Standard dev.)0.0007962472 (±0.009660193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8560.8560.856
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z342.400342.400342.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0970.2780.001

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Supplemental data

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Sample components

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Entire : ABC transporter, permease protein, Lipoprotein, ABC transporter, ...

EntireName: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding protein
Components
  • Complex: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding protein
    • Protein or peptide: ABC transporter, permease protein
    • Protein or peptide: Lipoprotein
    • Protein or peptide: ABC transporter, ATP-binding protein

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Supramolecule #1: ABC transporter, permease protein, Lipoprotein, ABC transporter, ...

SupramoleculeName: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria) / Strain: strain MC58

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Macromolecule #1: ABC transporter, permease protein

MacromoleculeName: ABC transporter, permease protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58
Molecular weightTheoretical: 24.363064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: ABC transporter, permease protein

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Macromolecule #2: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58
Molecular weightTheoretical: 33.010246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Lipoprotein

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Macromolecule #3: ABC transporter, ATP-binding protein

MacromoleculeName: ABC transporter, ATP-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58
Molecular weightTheoretical: 29.866152 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: ABC transporter, ATP-binding protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Number images used: 58434
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-7mbz:
Outward facing conformation of the MetNI methionine ABC transporter in complex with lipo-MetQ

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