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- EMDB-36938: Outward-facing structure of human ABCB6 W546A mutant (ADP/VO4-bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-36938
TitleOutward-facing structure of human ABCB6 W546A mutant (ADP/VO4-bound)
Map data
Sample
  • Organelle or cellular component: ATP-binding cassette sub-family B member 6 - Homo sapiens
    • Protein or peptide: ATP-binding cassette sub-family B member 6
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
KeywordsATP-Binding Cassette transporter / mitochondrial transporter / outward-facing state / ADP/VO4-bound / ABCB6 / MEMBRANE PROTEIN / TRANSPORT 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 / porphyrin-containing compound biosynthetic process / heme transport ...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 / porphyrin-containing compound biosynthetic process / heme transport / melanosome assembly / ABC-type heme transporter activity / heme transmembrane transport / 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 / mitochondrial outer membrane / intracellular iron ion homeostasis / endosome / Golgi membrane / lysosomal membrane / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / 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: 3.9 Å
AuthorsJin MS / Lee SS / Park JG / Jang E / Choi SH / Kim S / Kim JW
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4022846 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A2C1091278 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2023
Title: W546 stacking disruption traps the human porphyrin transporter ABCB6 in an outward-facing transient state.
Authors: Sang Soo Lee / Jun Gyou Park / Eunhong Jang / Seung Hun Choi / Subin Kim / Ji Won Kim / Mi Sun Jin /
Abstract: Human ATP-binding cassette transporter subfamily B6 (ABCB6) is a mitochondrial ATP-driven pump that translocates porphyrins from the cytoplasm into mitochondria for heme biosynthesis. Within the ...Human ATP-binding cassette transporter subfamily B6 (ABCB6) is a mitochondrial ATP-driven pump that translocates porphyrins from the cytoplasm into mitochondria for heme biosynthesis. Within the transport pathway, a conserved aromatic residue W546 located in each monomer plays a pivotal role in stabilizing the occluded conformation via π-stacking interactions. Herein, we employed cryo-electron microscopy to investigate the structural consequences of a single W546A mutation in ABCB6, both in detergent micelles and nanodiscs. The results demonstrate that the W546A mutation alters the conformational dynamics of detergent-purified ABCB6, leading to entrapment of the transporter in an outward-facing transient state. However, in the nanodisc system, we observed a direct interaction between the transporter and a phospholipid molecule that compensates for the absence of the W546 residue, thereby facilitating the normal conformational transition of the transporter toward the occluded state following ATP hydrolysis. The findings also reveal that adoption of the outward-facing conformation causes charge repulsion between ABCB6 and the bound substrate, and rearrangement of key interacting residues at the substrate-binding site. Consequently, the affinity for the substrate is significantly reduced, facilitating its release from the transporter.
History
DepositionJul 26, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36938.png

Downloads & links

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Map

FileDownload / File: emd_36938.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 230 pix.
= 195.73 Å		0.85 Å/pix.
x 230 pix.
= 195.73 Å		0.85 Å/pix.
x 230 pix.
= 195.73 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-0.7837791 - 1.0213846
Average (Standard dev.)0.003889776 (±0.041191142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 195.73 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36938_half_map_1.map
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Half map: #1

Fileemd_36938_half_map_2.map
Projections & Slices
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Sample components

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Entire : ATP-binding cassette sub-family B member 6 - Homo sapiens

EntireName: ATP-binding cassette sub-family B member 6 - Homo sapiens
Components
  • Organelle or cellular component: ATP-binding cassette sub-family B member 6 - Homo sapiens
    • Protein or peptide: ATP-binding cassette sub-family B member 6
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ATP-binding cassette sub-family B member 6 - Homo sapiens

SupramoleculeName: ATP-binding cassette sub-family B member 6 - Homo sapiens
type: organelle_or_cellular_component / 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

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: 65.869797 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: RDFGRKLRLL SGYLWPRGSP ALQLVVLICL GLMGLERALN VLVPIFYRNI VNLLTEKAPW NSLAWTVTSY VFLKFLQGGG TGSTGFVSN LRTFLWIRVQ QFTSRRVELL IFSHLHELSL RWHLGRRTGE VLRIADRGTS SVTGLLSYLV FNVIPTLADI I IGIIYFSM ...String:
RDFGRKLRLL SGYLWPRGSP ALQLVVLICL GLMGLERALN VLVPIFYRNI VNLLTEKAPW NSLAWTVTSY VFLKFLQGGG TGSTGFVSN LRTFLWIRVQ QFTSRRVELL IFSHLHELSL RWHLGRRTGE VLRIADRGTS SVTGLLSYLV FNVIPTLADI I IGIIYFSM FFNAWFGLIV FLCMSLYLTL TIVVTEWRTK FRRAMNTQEN ATRARAVDSL LNFETVKYYN AESYEVERYR EA IIKYQGL EWKSSASLVL LNQTQNLVIG LGLLAGSLLC AYFVTEQKLQ VGDYVLFGTY IIQLYMPLNA FGTYYRMIQT NFI DMENMF DLLKEETEVK DLPGAGPLRF QKGRIEFENV HFSYADGRET LQDVSFTVMP GQTLALVGPS GAGKSTILRL LFRF YDISS GCIRIDGQDI SQVTQASLRS HIGVVPQDTV LFNDTIADNI RYGRVTAGND EVEAAAQAAG IHDAIMAFPE GYRTQ VGER GLKLSGGEKQ RVAIARTILK APGIILLDEA TSALDTSNER AIQASLAKVC ANRTTIVVAH RLSTVVNADQ ILVIKD GCI VERGRHEALL SRGGVYADMW QLQQ

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

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / 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 #3: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration4 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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