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- PDB-7vgf: cryo-EM structure of AMP-PNP bound human ABCB7 -

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Entry
Database: PDB / ID: 7vgf
Titlecryo-EM structure of AMP-PNP bound human ABCB7
ComponentsIron-sulfur clusters transporter ABCB7, mitochondrial
KeywordsMEMBRANE PROTEIN / transporter / dimer / mitochondrial
Function / homology
Function and homology information


ABC-type iron-sulfur cluster transporter activity / positive regulation of iron-sulfur cluster assembly / iron-sulfur cluster export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / heme transmembrane transporter activity / iron ion transmembrane transport / Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity ...ABC-type iron-sulfur cluster transporter activity / positive regulation of iron-sulfur cluster assembly / iron-sulfur cluster export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / heme transmembrane transporter activity / iron ion transmembrane transport / Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / negative regulation of reactive oxygen species biosynthetic process / transmembrane transport / intracellular iron ion homeostasis / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
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. ...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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Iron-sulfur clusters transporter ABCB7, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYan, Q. / Yang, X. / Shen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870736 China
CitationJournal: J Struct Biol / Year: 2022
Title: Cryo-EM structure of AMP-PNP-bound human mitochondrial ATP-binding cassette transporter ABCB7.
Authors: Qinqin Yan / Yuequan Shen / Xue Yang /
Abstract: ATP-binding cassette subfamily B member 7 (ABCB7) is localized in the inner membrane of mitochondria, playing a critical role in iron metabolism. Here, we determined the structure of the ...ATP-binding cassette subfamily B member 7 (ABCB7) is localized in the inner membrane of mitochondria, playing a critical role in iron metabolism. Here, we determined the structure of the nonhydrolyzable ATP analog adenosine-5'-(β-γ-imido) triphosphate (AMP-PNP) bound human ABCB7 at 3.3 Å by single-particle electron cryo-microscopy (cryo-EM). The AMP-PNP-bound human ABCB7 shows an inverted V-shaped homodimeric architecture with an inward-facing open conformation. One AMP-PNP molecule and Mg were identified in each nucleotide-binding domain (NBD) of the hABCB7 monomer. Moreover, four disease-causing missense mutations of human ABCB7 have been mapped to the structure, creating a hotspot map for X-linked sideroblastic anemia and ataxia disease. Our results provide a structural basis for further understanding the transport mechanism of the mitochondrial ABC transporter.
History
DepositionSep 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Iron-sulfur clusters transporter ABCB7, mitochondrial
B: Iron-sulfur clusters transporter ABCB7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,8216
Polymers153,7602
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12060 Å2
ΔGint-86 kcal/mol
Surface area52150 Å2

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Components

#1: Protein Iron-sulfur clusters transporter ABCB7, mitochondrial / ATP-binding cassette sub-family B member 7 / mitochondrial / ATP-binding cassette transporter 7 / ...ATP-binding cassette sub-family B member 7 / mitochondrial / ATP-binding cassette transporter 7 / ABC transporter 7 protein


Mass: 76879.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB7, ABC7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75027
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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 ABCB7 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 150 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.5 / Details: 1 mM MgCl2 and 5 mM AMP-PNP
SpecimenConc.: 14 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM softwareName: cryoSPARC / Version: 3 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39927 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048422
ELECTRON MICROSCOPYf_angle_d0.72611462
ELECTRON MICROSCOPYf_dihedral_angle_d13.6532926
ELECTRON MICROSCOPYf_chiral_restr0.0411378
ELECTRON MICROSCOPYf_plane_restr0.0061456

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