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- EMDB-69143: Cryo-EM structure of human ABCB7 in complex with CoPP:GSH/ADPVO4 -

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Basic information

Entry
Database: EMDB / ID: EMD-69143
TitleCryo-EM structure of human ABCB7 in complex with CoPP:GSH/ADPVO4
Map data
Sample
  • Complex: Homodimer complex of ATP-binding cassette transporter B7 in complex with CoPP:GSH/ADPVO4
    • Protein or peptide: Iron-sulfur clusters transporter ABCB7, mitochondrial
  • Ligand: PROTOPORPHYRIN IX CONTAINING CO
  • Ligand: CHLORIDE ION
  • Ligand: Glutathione
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
KeywordsABCB7 / heme exporter / X-linked sideroblastic anemia with ataxia / cobalt protoporphyrin IX / iron-sulfur (Fe-S) cluster / glutathione / Membrane protein
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
Iron-sulfur clusters transporter ABCB7, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsJu S / Choi SH / Lee HY / Jin MS
Funding support Korea, Republic Of, 4 items
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, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69143.png

Downloads & links

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Map

FileDownload / File: emd_69143.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 380 pix.
= 288.8 Å		0.76 Å/pix.
x 380 pix.
= 288.8 Å		0.76 Å/pix.
x 380 pix.
= 288.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.146
Minimum - Maximum-0.6224241 - 1.1463659
Average (Standard dev.)-0.00008117277 (±0.023696193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 288.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_69143_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_69143_half_map_2.map
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Sample components

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Entire : Homodimer complex of ATP-binding cassette transporter B7 in compl...

EntireName: Homodimer complex of ATP-binding cassette transporter B7 in complex with CoPP:GSH/ADPVO4
Components
  • Complex: Homodimer complex of ATP-binding cassette transporter B7 in complex with CoPP:GSH/ADPVO4
    • Protein or peptide: Iron-sulfur clusters transporter ABCB7, mitochondrial
  • Ligand: PROTOPORPHYRIN IX CONTAINING CO
  • Ligand: CHLORIDE ION
  • Ligand: Glutathione
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION

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Supramolecule #1: Homodimer complex of ATP-binding cassette transporter B7 in compl...

SupramoleculeName: Homodimer complex of ATP-binding cassette transporter B7 in complex with CoPP:GSH/ADPVO4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 149 kDa/nm

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

MacromoleculeName: Iron-sulfur clusters transporter ABCB7, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.987109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KGNSGQFLDA AKALQVWPLI EKRTCWHGHA GGGLHTDPKE GLKDVDTRKI IKAMLSYVWP KDRPDLRARV AISLGFLGGA KAMNIVVPF MFKYAVDSLN QMSGNMLNLS DAPNTVATMA TAVLIGYGVS RAGAAFFNEV RNAVFGKVAQ NSIRRIAKNV F LHLHNLDL ...String:
KGNSGQFLDA AKALQVWPLI EKRTCWHGHA GGGLHTDPKE GLKDVDTRKI IKAMLSYVWP KDRPDLRARV AISLGFLGGA KAMNIVVPF MFKYAVDSLN QMSGNMLNLS DAPNTVATMA TAVLIGYGVS RAGAAFFNEV RNAVFGKVAQ NSIRRIAKNV F LHLHNLDL GFHLSRQTGA LSKAIDRGTR GISFVLSALV FNLLPIMFEV MLVSGVLYYK CGAQFALVTL GTLGTYTAFT VA VTRWRTR FRIEMNKADN DAGNAAIDSL LNYETVKYFN NERYEAQRYD GFLKTYETAS LKSTSTLAML NFGQSAIFSV GLT AIMVLA SQGIVAGTLT VGDLVMVNGL LFQLSLPLNF LGTVYRETRQ ALIDMNTLFT LLKVDTQIKD KVMASPLQIT PQTA TVAFD NVHFEYIEGQ KVLSGISFEV PAGKKVAIVG GSGSGKSTIV RLLFRFYEPQ KGSIYLAGQN IQDVSLESLR RAVGV VPQD AVLFHNTIYY NLLYGNISAS PEEVYAVAKL AGLHDAILRM PHGYDTQVGE RGLKLSGGEK QRVAIARAIL KDPPVI LYD EATSSLDSIT EETILGAMKD VVKHRTSIFI AHRLSTVVDA DEIIVLDQGK VAERGTHHGL LANPHSIYSE MWHTQSS RV QNHDNPKWEA KKENISKEEE RKKLQEEIVN SVKGCGNCSC

UniProtKB: Iron-sulfur clusters transporter ABCB7, mitochondrial

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING CO

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING CO / type: ligand / ID: 2 / Number of copies: 14 / Formula: COH
Molecular weightTheoretical: 619.575 Da
Chemical component information

ChemComp-COH:
PROTOPORPHYRIN IX CONTAINING CO

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: Glutathione

MacromoleculeName: Glutathione / type: ligand / ID: 4 / Number of copies: 2 / Formula: GSH
Molecular weightTheoretical: 307.323 Da
Chemical component information

ChemComp-GSH:
GLUTATHIONE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.0) / Number images used: 204460
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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