9NXC | pdb_00009nxc

Cryo-EM structure of a bacterial prototype ATP-binding cassette transporter MalFGK2.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides.

Ren, Q.Wang, J.Idikuda, V.Zhang, S.Shin, J.Ludlam, W.G.Real Hernandez, L.M.Zdancewicz, S.Kreutzberger, A.J.B.Chang, H.Kiessling, V.Tamm, L.K.Jomaa, A.Levental, I.Martemyanov, K.Chanda, B.Bao, H.

(2025) Nat Commun 16: 7973-7973

  • DOI: https://doi.org/10.1038/s41467-025-63275-8
  • Primary Citation of Related Structures:  
    9BCR, 9NQJ, 9NXC

  • PubMed Abstract: 

    Membrane scaffold protein-based nanodiscs have facilitated unprecedented structural and biophysical analysis of membrane proteins in a near-native lipid environment. However, successful reconstitution of membrane proteins in nanodiscs requires prior solubilization and purification in detergents, which may impact their physiological structure and function. Furthermore, the detergent-mediated reconstitution of nanodiscs is unlikely to recapitulate the precise composition or asymmetry of native membranes. To circumvent this fundamental limitation of traditional nanodisc technology, we herein describe the development of membrane-solubilizing peptides to directly extract membrane proteins from native cell membranes into nanoscale discoids. By systematically protein engineering and screening, we create a class of chemically modified Apolipoprotein-A1 mimetic peptides to enable the formation of detergent-free nanodiscs with high efficiency. Nanodiscs generated with these engineered membrane scaffold peptides are suitable for obtaining high-resolution structures using single-particle cryo-EM with native lipids. To further highlight the versatility of our approach, we directly extract a sampling of membrane signaling proteins with their surrounding native membranes for biochemical and biophysical interrogations.


  • Organizational Affiliation
    • Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, Florida, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin transport system permease protein MalFA [auth H]519Escherichia coliMutation(s): 0 
Gene Names: malFc5003
Membrane Entity: Yes 
UniProt
Find proteins for Q8FB38 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore Q8FB38 
Go to UniProtKB:  Q8FB38
Entity Groups  
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UniProt GroupQ8FB38
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin transport system permease protein MalGB [auth I]286Escherichia coliMutation(s): 0 
Gene Names: malGZ5630ECs5015
Membrane Entity: Yes 
UniProt
Find proteins for P68185 (Escherichia coli O157:H7)
Explore P68185 
Go to UniProtKB:  P68185
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UniProt GroupP68185
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin import ATP-binding protein MalK371Escherichia coliMutation(s): 0 
Gene Names: malKZ5633ECs5018
EC: 7.5.2.1
Membrane Entity: Yes 
UniProt
Find proteins for P68188 (Escherichia coli O157:H7)
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Go to UniProtKB:  P68188
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UniProt GroupP68188
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin import ATP-binding protein MalK373Escherichia coliMutation(s): 0 
Gene Names: malKZ5633ECs5018
EC: 7.5.2.1
Membrane Entity: Yes 
UniProt
Find proteins for P68188 (Escherichia coli O157:H7)
Explore P68188 
Go to UniProtKB:  P68188
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68188
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM140920

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release