7E7Q | pdb_00007e7q

Cryo-EM structure of human ABCA4 in ATP-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7E7Q

This is version 1.3 of the entry. See complete history

Literature

Structural basis of substrate recognition and translocation by human ABCA4.

Xie, T.Zhang, Z.Fang, Q.Du, B.Gong, X.

(2021) Nat Commun 12: 3853-3853

  • DOI: https://doi.org/10.1038/s41467-021-24194-6
  • Primary Citation Related Structures: 
    7E7I, 7E7O, 7E7Q

  • PubMed Abstract: 

    Human ATP-binding cassette (ABC) subfamily A (ABCA) transporters mediate the transport of various lipid compounds across the membrane. Mutations in human ABCA transporters have been described to cause severe hereditary disorders associated with impaired lipid transport. However, little is known about the mechanistic details of substrate recognition and translocation by ABCA transporters. Here, we present three cryo-EM structures of human ABCA4, a retina-specific ABCA transporter, in distinct functional states at resolutions of 3.3-3.4 Å. In the nucleotide-free state, the two transmembrane domains (TMDs) exhibit a lateral-opening conformation, allowing the lateral entry of substrate from the lipid bilayer. The N-retinylidene-phosphatidylethanolamine (NRPE), the physiological lipid substrate of ABCA4, is sandwiched between the two TMDs in the luminal leaflet and is further stabilized by an extended loop from extracellular domain 1. In the ATP-bound state, the two TMDs display a closed conformation, which precludes the substrate binding. Our study provides a molecular basis to understand the mechanism of ABCA4-mediated NRPE recognition and translocation, and suggests a common 'lateral access and extrusion' mechanism for ABCA-mediated lipid transport.


  • Organizational Affiliation
    • Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.

Macromolecule Content 

  • Total Structure Weight: 265.57 kDa 
  • Atom Count: 15,279 
  • Modeled Residue Count: 1,958 
  • Deposited Residue Count: 2,317 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinal-specific phospholipid-transporting ATPase ABCA42,317Homo sapiensMutation(s): 2 
Gene Names: ABCA4ABCR
EC: 7.6.2.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P78363 (Homo sapiens)
Explore P78363 
Go to UniProtKB:  P78363
PHAROS:  P78363
GTEx:  ENSG00000198691 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78363
Glycosylation
Glycosylation Sites: 9Go to GlyGen: P78363-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth D],
C [auth M]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G89225LT
GlyCosmos: G89225LT
GlyGen: G89225LT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection