9NQJ | pdb_00009nqj

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 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 import ATP-binding protein MalK
A, B
371Escherichia coli K-12Mutation(s): 0 
Gene Names: malKb4035JW3995
EC: 7.5.2.1
Membrane Entity: Yes 
UniProt
Find proteins for P68187 (Escherichia coli (strain K12))
Explore P68187 
Go to UniProtKB:  P68187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68187
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin transport system permease protein MalFC [auth F]514Escherichia coli K-12Mutation(s): 0 
Gene Names: malFb4033JW3993
Membrane Entity: Yes 
UniProt
Find proteins for P02916 (Escherichia coli (strain K12))
Explore P02916 
Go to UniProtKB:  P02916
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02916
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin transport system permease protein MalGD [auth G]296Escherichia coli K-12Mutation(s): 0 
Gene Names: malGb4032JW3992
Membrane Entity: Yes 
UniProt
Find proteins for P68183 (Escherichia coli (strain K12))
Explore P68183 
Go to UniProtKB:  P68183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68183
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
VO4 (Subject of Investigation/LOI)
Query on VO4

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A]
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.2_4487

Structure Validation

View Full Validation Report



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