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- PDB-7d7r: Cryo-EM structure of the core domain of human ABCB6 transporter -

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Basic information

Entry
Database: PDB / ID: 7d7r
TitleCryo-EM structure of the core domain of human ABCB6 transporter
ComponentsATP-binding cassette sub-family B member 6, mitochondrial
KeywordsMEMBRANE PROTEIN / Transporter / Dimer / Porphyrins / Heme
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsWang, C. / Cao, C. / Wang, N. / Wang, X. / Zhang, X.C.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030301 China
Chinese Academy of SciencesXDB08020301 China
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Protein Sci / Year: 2020
Title: Cryo-electron microscopy structure of human ABCB6 transporter.
Authors: Chunyu Wang / Can Cao / Nan Wang / Xiangxi Wang / Xianping Wang / Xuejun C Zhang /
Abstract: Human ATP-binding cassette transporter 6 of subfamily B (ABCB6) is an ABC transporter involved in the translocation toxic metals and anti-cancer drugs. Using cryo-electron microscopy, we determined ...Human ATP-binding cassette transporter 6 of subfamily B (ABCB6) is an ABC transporter involved in the translocation toxic metals and anti-cancer drugs. Using cryo-electron microscopy, we determined the molecular structure of full-length ABCB6 in an apo state. The structure of ABCB6 unravels the architecture of a full-length ABCB transporter that harbors two N-terminal transmembrane domains which is indispensable for its ATPase activity in our in vitro assay. A slit-like substrate binding pocket of ABCB6 may accommodate the planar shape of porphyrins, and the existence of a secondary cavity near the mitochondrial intermembrane space side would further facilitate substrate release. Furthermore, the ATPase activity of ABCB6 stimulated with a variety of porphyrin substrates showed different profiles in the presence of glutathione (GSH), suggesting the action of a distinct substrate translocation mechanism depending on the use of GSH as a cofactor.
History
DepositionOct 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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


Theoretical massNumber of molelcules
Total (without water)187,9482
Polymers187,9482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLYA1 - 580
d_21ens_1ASPGLYB1 - 580

NCS oper: (Code: givenMatrix: (-0.999997529815, 0.00164410469309, -0.00149575532574), (-0.00164268660531, -0.999998200669, -0.000948809747209), (-0.00149731257694, -0.000946350346235, 0.999998431237) ...NCS oper: (Code: given
Matrix: (-0.999997529815, 0.00164410469309, -0.00149575532574), (-0.00164268660531, -0.999998200669, -0.000948809747209), (-0.00149731257694, -0.000946350346235, 0.999998431237)
Vector: 85.2953026029, 106.281886647, 0.0895089532817)

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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): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9NP58

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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: Human ABCB6 protein homodimer. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74135 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00427786
ELECTRON MICROSCOPYf_angle_d0.955810642
ELECTRON MICROSCOPYf_chiral_restr0.05361300
ELECTRON MICROSCOPYf_plane_restr0.00591394
ELECTRON MICROSCOPYf_dihedral_angle_d22.93292374
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.0513074167806 Å

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