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- PDB-7mbz: Outward facing conformation of the MetNI methionine ABC transport... -

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Basic information

Entry
Database: PDB / ID: 7mbz
TitleOutward facing conformation of the MetNI methionine ABC transporter in complex with lipo-MetQ
Components
  • ABC transporter, ATP-binding protein
  • ABC transporter, permease protein
  • Lipoprotein
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsSharaf, N.G. / Rees, D.C.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Data processing / Category: em_3d_reconstruction / Item: _em_3d_reconstruction.resolution
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: ABC transporter, permease protein
E: Lipoprotein
B: ABC transporter, permease protein
C: ABC transporter, ATP-binding protein
D: ABC transporter, ATP-binding protein


Theoretical massNumber of molelcules
Total (without water)141,4695
Polymers141,4695
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12010 Å2
ΔGint-42 kcal/mol
Surface area53140 Å2

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Components

#1: Protein ABC transporter, permease protein


Mass: 24363.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: NMB1947 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q9JXP3
#2: Protein Lipoprotein


Mass: 33010.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: NMB1946 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q7DD63
#3: Protein ABC transporter, ATP-binding protein


Mass: 29866.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: NMB1948 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q9JXP2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ABC transporter, permease protein, Lipoprotein, ABC transporter, ATP-binding protein
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: YES
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria) / Strain: strain MC58
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
12Cootmodel fitting
25ISOLDEmodel refinement
26Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.4 Å / Num. of particles: 58434 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient

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