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- EMDB-39534: Cryo-EM structure of the human ABCB6 in complex with Cd(II):GSH -

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Basic information

Entry
Database: EMDB / ID: EMD-39534
TitleCryo-EM structure of the human ABCB6 in complex with Cd(II):GSH
Map data
Sample
  • Complex: Homodimer complex of ATP-binding cassette transporter B6 in complex with Cd(II):GSH
    • Protein or peptide: ATP-binding cassette sub-family B member 6
  • Ligand: GLUTATHIONE
  • Ligand: CADMIUM ION
KeywordsCryo-EM / ABC transporter / ATP-binding cassette transporter B6 / ABCB6 / heme biosynthesis / heavy metal detoxification / glutathione / phytochelatin / MEMBRANE PROTEIN
Function / homology
Function and homology information


cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / heme transmembrane transport / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / ABC-type heme transporter activity / porphyrin-containing compound metabolic process / heme transport / tetrapyrrole binding ...cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / heme transmembrane transport / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / ABC-type heme transporter activity / porphyrin-containing compound metabolic process / heme transport / tetrapyrrole binding / heme metabolic process / porphyrin-containing compound biosynthetic process / melanosome assembly / melanosome membrane / multivesicular body membrane / mitochondrial envelope / endolysosome membrane / vacuolar membrane / skin development / efflux transmembrane transporter activity / intracellular copper ion homeostasis / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / brain development / transmembrane transport / early endosome membrane / intracellular iron ion homeostasis / mitochondrial outer membrane / endosome / lysosomal membrane / Golgi membrane / heme binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / 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 ...Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / 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
ATP-binding cassette sub-family B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChoi SH / Lee SS / Lee HY / Kim S / Kim JW / Jin MS
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021M3A9I4022846 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1A2C1091278 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2024
Title: Cryo-EM structure of cadmium-bound human ABCB6.
Authors: Seung Hun Choi / Sang Soo Lee / Hyeon You Lee / Subin Kim / Ji Won Kim / Mi Sun Jin /
Abstract: ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy ...ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy structures of human ABCB6 bound to a cadmium Cd(II) ion in the presence of antioxidant thiol peptides glutathione (GSH) and phytochelatin 2 (PC2) at resolutions of 3.2 and 3.1 Å, respectively. The overall folding of the two structures resembles the inward-facing apo state but with less separation between the two halves of the transporter. Two GSH molecules are symmetrically bound to the Cd(II) ion in a bent conformation, with the central cysteine protruding towards the metal. The N-terminal glutamate and C-terminal glycine of GSH do not directly interact with Cd(II) but contribute to neutralizing positive charges of the binding cavity by forming hydrogen bonds and van der Waals interactions with nearby residues. In the presence of PC2, Cd(II) binding to ABCB6 is similar to that observed with GSH, except that two cysteine residues of each PC2 molecule participate in Cd(II) coordination to form a tetrathiolate. Structural comparison of human ABCB6 and its homologous Atm-type transporters indicate that their distinct substrate specificity might be attributed to variations in the capping residues situated at the top of the substrate-binding cavity.
History
DepositionMar 20, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39534.png

Downloads & links

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Map

FileDownload / File: emd_39534.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.15945992 - 0.353605
Average (Standard dev.)0.0010247008 (±0.015874768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39534_half_map_1.map
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Half map: #2

Fileemd_39534_half_map_2.map
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Sample components

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Entire : Homodimer complex of ATP-binding cassette transporter B6 in compl...

EntireName: Homodimer complex of ATP-binding cassette transporter B6 in complex with Cd(II):GSH
Components
  • Complex: Homodimer complex of ATP-binding cassette transporter B6 in complex with Cd(II):GSH
    • Protein or peptide: ATP-binding cassette sub-family B member 6
  • Ligand: GLUTATHIONE
  • Ligand: CADMIUM ION

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Supramolecule #1: Homodimer complex of ATP-binding cassette transporter B6 in compl...

SupramoleculeName: Homodimer complex of ATP-binding cassette transporter B6 in complex with Cd(II):GSH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 143.2 kDa/nm

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Macromolecule #1: ATP-binding cassette sub-family B member 6

MacromoleculeName: ATP-binding cassette sub-family B member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type heme transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.719039 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: APGLRPQSYT LQVHEEDQDV ERSQVRSAAQ QSTWRDFGRK LRLLSGYLWP RGSPALQLVV LICLGLMGLE RALNVLVPIF YRNIVNLLT EKAPWNSLAW TVTSYVFLKF LQGGGTGSTG FVSNLRTFLW IRVQQFTSRR VELLIFSHLH ELSLRWHLGR R TGEVLRIA ...String:
APGLRPQSYT LQVHEEDQDV ERSQVRSAAQ QSTWRDFGRK LRLLSGYLWP RGSPALQLVV LICLGLMGLE RALNVLVPIF YRNIVNLLT EKAPWNSLAW TVTSYVFLKF LQGGGTGSTG FVSNLRTFLW IRVQQFTSRR VELLIFSHLH ELSLRWHLGR R TGEVLRIA DRGTSSVTGL LSYLVFNVIP TLADIIIGII YFSMFFNAWF GLIVFLCMSL YLTLTIVVTE WRTKFRRAMN TQ ENATRAR AVDSLLNFET VKYYNAESYE VERYREAIIK YQGLEWKSSA SLVLLNQTQN LVIGLGLLAG SLLCAYFVTE QKL QVGDYV LFGTYIIQLY MPLNWFGTYY RMIQTNFIDM ENMFDLLKEE TEVKDLPGAG PLRFQKGRIE FENVHFSYAD GRET LQDVS FTVMPGQTLA LVGPSGAGKS TILRLLFRFY DISSGCIRID GQDISQVTQA SLRSHIGVVP QDTVLFNDTI ADNIR YGRV TAGNDEVEAA AQAAGIHDAI MAFPEGYRTQ VGERGLKLSG GEKQRVAIAR TILKAPGIIL LDEATSALDT SNERAI QAS LAKVCANRTT IVVAHRLSTV VNADQILVIK DGCIVERGRH EALLSRGGVY ADMWQLQQGQ EETSEDTKPQ TMER

UniProtKB: ATP-binding cassette sub-family B member 6

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Macromolecule #2: GLUTATHIONE

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

ChemComp-GSH:
GLUTATHIONE

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Macromolecule #3: CADMIUM ION

MacromoleculeName: CADMIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CD
Molecular weightTheoretical: 112.411 Da

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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: 7
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 TALOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 402369
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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