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- PDB-7dnz: Cryo-EM structure of the human ABCB6 (Hemin and GSH-bound) -

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Basic information

Entry
Database: PDB / ID: 7dnz
TitleCryo-EM structure of the human ABCB6 (Hemin and GSH-bound)
ComponentsATP-binding cassette sub-family B member 6, mitochondrial
KeywordsMEMBRANE PROTEIN / ABCB6 / heme transporter
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 / tetrapyrrole binding / heme transport ...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 / tetrapyrrole binding / heme transport / 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
GLUTATHIONE / PROTOPORPHYRIN IX CONTAINING FE / CHOLESTEROL HEMISUCCINATE / ATP-binding cassette sub-family B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKim, S. / Lee, S.S. / Park, J.G. / Kim, J.W. / Kim, S. / Kim, N.J. / Hong, S. / Kang, J.Y. / Jin, M.S.
Funding support Korea, Republic Of, 4items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-binding cassette sub-family B member 6, mitochondrial
B: ATP-binding cassette sub-family B member 6, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,71413
Polymers187,9482
Non-polymers4,76611
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ATP-binding cassette sub-family B member 6, mitochondrial / Mitochondrial ABC transporter 3 / Mt-ABC transporter 3 / P-glycoprotein-related protein / ...Mitochondrial ABC transporter 3 / Mt-ABC transporter 3 / P-glycoprotein-related protein / Ubiquitously-expressed mammalian ABC half transporter


Mass: 93974.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB6, MTABC3, PRP, UMAT / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NP58
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: ABCB6 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Cell: BTI-Tn-5B1-4
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaClSodium chloride1
20.056 %CYMAL-6C24H44O111
30.056 %Cholesteryl Hemisuccinate Tris SaltC31H50O4C4H11NO31
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2600 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

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
10RELION3.1initial Euler assignment
11cryoSPARC2.15.0final Euler assignment
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 283866 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089874
ELECTRON MICROSCOPYf_angle_d1.09713432
ELECTRON MICROSCOPYf_dihedral_angle_d15.6191540
ELECTRON MICROSCOPYf_chiral_restr0.0581554
ELECTRON MICROSCOPYf_plane_restr0.0061674

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