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- PDB-23pi: Cryo-EM structure of the human ABCB7 in occluded state -

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Basic information

Entry
Database: PDB / ID: 23pi
TitleCryo-EM structure of the human ABCB7 in occluded state
ComponentsIron-sulfur clusters transporter ABCB7, mitochondrial
KeywordsMEMBRANE PROTEIN / ABCB7 / heme exporter / X-linked sideroblastic anemia with ataxia / cobalt protoporphyrin IX / iron-sulfur (Fe-S) cluster / glutathione
Function / homology
Function and homology information


ABC-type iron-sulfur cluster transporter activity / positive regulation of iron-sulfur cluster assembly / iron-sulfur cluster export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / heme transmembrane transporter activity / Cytosolic iron-sulfur cluster assembly / iron ion transmembrane transport / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity ...ABC-type iron-sulfur cluster transporter activity / positive regulation of iron-sulfur cluster assembly / iron-sulfur cluster export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / heme transmembrane transporter activity / Cytosolic iron-sulfur cluster assembly / iron ion transmembrane transport / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / negative regulation of reactive oxygen species biosynthetic process / transmembrane transport / intracellular iron ion homeostasis / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PROTOPORPHYRIN IX CONTAINING CO / Iron-sulfur clusters transporter ABCB7, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsJu, S. / Choi, S.H. / Lee, H.Y. / Jin, M.S.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2021-NR056576 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00344154 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00440614 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00406670 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structures of human ABCB7 reveal the molecular basis of mitochondrial matrix heme export.
Authors: Seulgi Ju / Seung Hun Choi / Hyeon You Lee / Mi Sun Jin /
Abstract: ATP-binding cassette transporter subfamily B member 7 (ABCB7) is a mitochondrial ATP-driven pump essential for cytosolic iron-sulfur (Fe-S) cluster biogenesis and cellular iron homeostasis. Mutations ...ATP-binding cassette transporter subfamily B member 7 (ABCB7) is a mitochondrial ATP-driven pump essential for cytosolic iron-sulfur (Fe-S) cluster biogenesis and cellular iron homeostasis. Mutations in ABCB7 are linked to X-linked sideroblastic anemia with ataxia (XLSA/A). Here, we demonstrate that the ATPase activity of ABCB7 is stimulated by iron and cobalt protoporphyrin IX (hemin and CoPP) in the presence of glutathione (GSH), highlighting an additional role for ABCB7 as a metalloporphyrin exporter. Using single-particle cryo-electron microscopy, we determine the structures of human ABCB7 in multiple functional states at resolutions of up to 2.3 Å. Our structures reveal a putative substrate-binding cavity that accommodates two stacked CoPP molecules conjugated by two GSH cysteine thiols. The conserved residue F426 controls substrate entrapment and release as a molecular gate. We further show that at high substrate concentrations excess CoPP easily partitions into the lipid bilayer, where the hydrophobic environment stabilizes the porphyrin macrocycle and limits the aggregation or redox reactivity that is prone to occur with free porphyrins in aqueous solution. Finally, our structure analyses rationalize the pathogenic effect of the E433K mutation associated with XLSA/A disease.
History
DepositionFeb 12, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-sulfur clusters transporter ABCB7, mitochondrial
B: Iron-sulfur clusters transporter ABCB7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,75312
Polymers149,9722
Non-polymers4,78010
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Iron-sulfur clusters transporter ABCB7, mitochondrial


Mass: 74986.117 Da / Num. of mol.: 2 / Mutation: E634Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75027
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / 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
#4: Chemical
ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32CoN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: Homodimer complex of ATP-binding cassette transporter B7 in occluded state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 149.79 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.1particle selection
2PHENIX1.20.1_4487model refinement
5cryoSPARCv4.3.1CTF correction
13cryoSPARCv4.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 425646 / Symmetry type: POINT
RefinementHighest resolution: 2.33 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039138
ELECTRON MICROSCOPYf_angle_d0.58612490
ELECTRON MICROSCOPYf_dihedral_angle_d8.0211390
ELECTRON MICROSCOPYf_chiral_restr0.041411
ELECTRON MICROSCOPYf_plane_restr0.0051521

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