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- PDB-7w02: Cryo-EM structure of ATP-bound ABCA3 -

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Basic information

Entry
Database: PDB / ID: 7w02
TitleCryo-EM structure of ATP-bound ABCA3
ComponentsPhospholipid-transporting ATPase ABCA3
KeywordsTRANSLOCASE / ABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of protein homooligomerization / lamellar body membrane / Defective ABCA3 causes SMDP3 / Defective ABCA3 causes SMDP3 / regulation of phosphatidylcholine metabolic process / alveolar lamellar body membrane / phosphatidylcholine transfer activity / lamellar body / positive regulation of phospholipid transport / alveolar lamellar body ...positive regulation of protein homooligomerization / lamellar body membrane / Defective ABCA3 causes SMDP3 / Defective ABCA3 causes SMDP3 / regulation of phosphatidylcholine metabolic process / alveolar lamellar body membrane / phosphatidylcholine transfer activity / lamellar body / positive regulation of phospholipid transport / alveolar lamellar body / xenobiotic export from cell / organelle assembly / phosphatidylcholine flippase activity / ABC transporters in lipid homeostasis / phosphatidylglycerol metabolic process / regulation of lipid biosynthetic process / phosphatidylcholine metabolic process / positive regulation of phospholipid efflux / lipid transporter activity / Surfactant metabolism / xenobiotic transmembrane transport / phospholipid transport / phospholipid homeostasis / multivesicular body membrane / P-type phospholipid transporter / ABC-type xenobiotic transporter / surfactant homeostasis / ABC-type xenobiotic transporter activity / xenobiotic transport / lipid transport / positive regulation of cholesterol efflux / ATPase-coupled transmembrane transporter activity / response to glucocorticoid / cytoplasmic vesicle membrane / lung development / late endosome / response to xenobiotic stimulus / lysosomal membrane / intracellular membrane-bounded organelle / ATP hydrolysis activity / extracellular space / ATP binding / plasma membrane
Similarity search - Function
ABC transporter A / : / ABCA1-like, C-terminal R1 regulatory domain / ABC-2 family transporter protein / ABC-2 type transporter / 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. ...ABC transporter A / : / ABCA1-like, C-terminal R1 regulatory domain / ABC-2 family transporter protein / ABC-2 type transporter / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Phospholipid-transporting ATPase ABCA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXie, T. / Zhang, Z.K. / Yue, J. / Gong, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structures of the human surfactant lipid transporter ABCA3.
Authors: Tian Xie / Zike Zhang / Jian Yue / Qi Fang / Xin Gong /
Abstract: The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter ABCA3 plays a critical role in pulmonary surfactant biogenesis. Mutations in human ABCA3 have been recognized as the most ...The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter ABCA3 plays a critical role in pulmonary surfactant biogenesis. Mutations in human ABCA3 have been recognized as the most frequent causes of inherited surfactant dysfunction disorders. Despite two decades of research, in vitro biochemical and structural studies of ABCA3 are still lacking. Here, we report the cryo-EM structures of human ABCA3 in two distinct conformations, both at resolution of 3.3 Å. In the absence of ATP, ABCA3 adopts a "lateral-opening" conformation with the lateral surfaces of transmembrane domains (TMDs) exposed to the membrane and features two positively charged cavities within the TMDs as potential substrate binding sites. ATP binding induces pronounced conformational changes, resulting in the collapse of the potential substrate binding cavities. Our results help to rationalize the disease-causing mutations in human ABCA3 and suggest a conserved "lateral access and extrusion" mechanism for both lipid export and import mediated by ABCA transporters.
History
DepositionNov 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipid-transporting ATPase ABCA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,0177
Polymers196,5121
Non-polymers1,5056
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2350 Å2
ΔGint-25 kcal/mol
Surface area67630 Å2

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Components

#1: Protein Phospholipid-transporting ATPase ABCA3 / ABC-C transporter / ATP-binding cassette sub-family A member 3 / ATP-binding cassette transporter 3 ...ABC-C transporter / ATP-binding cassette sub-family A member 3 / ATP-binding cassette transporter 3 / ATP-binding cassette 3 / Xenobiotic-transporting ATPase ABCA3


Mass: 196511.688 Da / Num. of mol.: 1 / Mutation: E690Q, E1540Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCA3, ABC3 / Production host: Homo sapiens (human)
References: UniProt: Q99758, P-type phospholipid transporter, ABC-type xenobiotic transporter
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: ABCA3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80575 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612771
ELECTRON MICROSCOPYf_angle_d0.80617361
ELECTRON MICROSCOPYf_dihedral_angle_d25.8062033
ELECTRON MICROSCOPYf_chiral_restr0.0491987
ELECTRON MICROSCOPYf_plane_restr0.0042160

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