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- EMDB-30790: Cryo-EM structure of the human ABCB6 (coproporphyrin III-bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-30790
TitleCryo-EM structure of the human ABCB6 (coproporphyrin III-bound)
Map datagenerated from non-uniform refinement in cryosparc
Sample
  • Complex: ABCB6
    • Protein or peptide: ATP-binding cassette sub-family B member 6, mitochondrial
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: coproporphyrin III
KeywordsABCB6 / heme transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective ABCB6 causes MCOPCB7 / cellular detoxification of cadmium ion / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme metabolic process / heme transport / porphyrin-containing compound biosynthetic process ...Defective ABCB6 causes MCOPCB7 / cellular detoxification of cadmium ion / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme metabolic process / heme transport / porphyrin-containing compound biosynthetic process / melanosome assembly / heme transmembrane transport / ABC-type heme transporter activity / melanosome membrane / multivesicular body membrane / endolysosome membrane / mitochondrial envelope / 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: 3.4 Å
AuthorsKim S / Lee SS
Funding support Korea, Republic Of, 4 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029753 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020R1I1A1A01072077 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2019M3E5D6066058 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2019R1A6A1A10073887 Korea, Republic Of
CitationJournal: Mol Cells / Year: 2022
Title: Structural Insights into Porphyrin Recognition by the Human ATP-Binding Cassette Transporter ABCB6.
Authors: Songwon Kim / Sang Soo Lee / Jun Gyou Park / Ji Won Kim / Seulgi Ju / Seung Hun Choi / Subin Kim / Na Jin Kim / Semi Hong / Jin Young Kang / Mi Sun Jin /
Abstract: Human ABCB6 is an ATP-binding cassette transporter that regulates heme biosynthesis by translocating various porphyrins from the cytoplasm into the mitochondria. Here we report the cryo-electron ...Human ABCB6 is an ATP-binding cassette transporter that regulates heme biosynthesis by translocating various porphyrins from the cytoplasm into the mitochondria. Here we report the cryo-electron microscopy (cryo-EM) structures of human ABCB6 with its substrates, coproporphyrin III (CPIII) and hemin, at 3.5 and 3.7 Å resolution, respectively. Metalfree porphyrin CPIII binds to ABCB6 within the central cavity, where its propionic acids form hydrogen bonds with the highly conserved Y550. The resulting structure has an overall fold similar to the inward-facing apo structure, but the two nucleotide-binding domains (NBDs) are slightly closer to each other. In contrast, when ABCB6 binds a metal-centered porphyrin hemin in complex with two glutathione molecules (1 hemin: 2 glutathione), the two NBDs end up much closer together, aligning them to bind and hydrolyze ATP more efficiently. In our structures, a glycine-rich and highly flexible "bulge" loop on TM helix 7 undergoes significant conformational changes associated with substrate binding. Our findings suggest that ABCB6 utilizes at least two distinct mechanisms to fine-tune substrate specificity and transport efficiency.
History
DepositionDec 11, 2020-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_30790.png

Downloads & links

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Map

FileDownload / File: emd_30790.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgenerated from non-uniform refinement in cryosparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 340 pix.
= 223.04 Å		0.66 Å/pix.
x 340 pix.
= 223.04 Å		0.66 Å/pix.
x 340 pix.
= 223.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0559
Minimum - Maximum-0.24176593 - 0.3004375
Average (Standard dev.)0.00026779 (±0.009286174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 223.04001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ABCB6

EntireName: ABCB6
Components
  • Complex: ABCB6
    • Protein or peptide: ATP-binding cassette sub-family B member 6, mitochondrial
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: coproporphyrin III

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Supramolecule #1: ABCB6

SupramoleculeName: ABCB6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: ATP-binding cassette sub-family B member 6, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.974172 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVTVGNYCEA EGPVGPAWMQ DGLSPCFFFT LVPSTRMALG TLALVLALPC RRRERPAGAD SLSWGAGPRI SPYVLQLLLA TLQAALPLA GLAGRVGTAR GAPLPSYLLL ASVLESLAGA CGLWLLVVER SQARQRLAMG IWIKFRHSPG LLLLWTVAFA A ENLALVSW ...String:
MVTVGNYCEA EGPVGPAWMQ DGLSPCFFFT LVPSTRMALG TLALVLALPC RRRERPAGAD SLSWGAGPRI SPYVLQLLLA TLQAALPLA GLAGRVGTAR GAPLPSYLLL ASVLESLAGA CGLWLLVVER SQARQRLAMG IWIKFRHSPG LLLLWTVAFA A ENLALVSW NSPQWWWARA DLGQQVQFSL WVLRYVVSGG LFVLGLWAPG LRPQSYTLQV HEEDQDVERS QVRSAAQQST WR DFGRKLR LLSGYLWPRG SPALQLVVLI CLGLMGLERA LNVLVPIFYR NIVNLLTEKA PWNSLAWTVT SYVFLKFLQG GGT GSTGFV SNLRTFLWIR VQQFTSRRVE LLIFSHLHEL SLRWHLGRRT GEVLRIADRG TSSVTGLLSY LVFNVIPTLA DIII GIIYF SMFFNAWFGL IVFLCMSLYL TLTIVVTEWR TKFRRAMNTQ ENATRARAVD SLLNFETVKY YNAESYEVER YREAI IKYQ GLEWKSSASL VLLNQTQNLV IGLGLLAGSL LCAYFVTEQK LQVGDYVLFG TYIIQLYMPL NWFGTYYRMI QTNFID MEN MFDLLKEETE VKDLPGAGPL RFQKGRIEFE NVHFSYADGR ETLQDVSFTV MPGQTLALVG PSGAGKSTIL RLLFRFY DI SSGCIRIDGQ DISQVTQASL RSHIGVVPQD TVLFNDTIAD NIRYGRVTAG NDEVEAAAQA AGIHDAIMAF PEGYRTQV G ERGLKLSGGE KQRVAIARTI LKAPGIILLD EATSALDTSN ERAIQASLAK VCANRTTIVV AHRLSTVVNA DQILVIKDG CIVERGRHEA LLSRGGVYAD MWQLQQGQEE TSEDTKPQTM ER

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

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: coproporphyrin III

MacromoleculeName: coproporphyrin III / type: ligand / ID: 3 / Number of copies: 1 / Formula: HT9
Molecular weightTheoretical: 654.709 Da
Chemical component information

ChemComp-HT9:
coproporphyrin III

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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

Concentration6 mg/mL
BufferpH: 7 / Component - Concentration: 200.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mrp


Details: We also used PDB ID 3NH6 as a startup model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108637
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7dny:
Cryo-EM structure of the human ABCB6 (coproporphyrin III-bound)

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