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- EMDB-31967: cryo-EM structure of AMP-PNP bound human ABCB7 -

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Basic information

Entry
Database: EMDB / ID: EMD-31967
Titlecryo-EM structure of AMP-PNP bound human ABCB7
Map dataEM map
Sample
  • Complex: human ABCB7
    • Protein or peptide: Iron-sulfur clusters transporter ABCB7, mitochondrial
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordstransporter / dimer / mitochondrial / MEMBRANE PROTEIN
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
Iron-sulfur clusters transporter ABCB7, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYan Q / Yang X
Funding support China, 1 items
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, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vgf
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31967.png

Downloads & links

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Map

FileDownload / File: emd_31967.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.3
Minimum - Maximum-0.8740344 - 2.3293235
Average (Standard dev.)-0.001327276 (±0.059470788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.8742.329-0.001

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Supplemental data

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Sample components

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Entire : human ABCB7

EntireName: human ABCB7
Components
  • Complex: human ABCB7
    • Protein or peptide: Iron-sulfur clusters transporter ABCB7, mitochondrial
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: human ABCB7

SupramoleculeName: human ABCB7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 kDa/nm

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Macromolecule #1: Iron-sulfur clusters transporter ABCB7, mitochondrial

MacromoleculeName: Iron-sulfur clusters transporter ABCB7, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.879914 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGNSGQFLDA AKALQVWPLI EKRTCWHGHA GGGLHTDPKE GLKDVDTRKI IKAMLSYVWP KDRPDLRARV AISLGFLGGA KAMNIVVPF MFKYAVDSLN QMSGNMLNLS DAPNTVATMA TAVLIGYGVS RAGAAFFNEV RNAVFGKVAQ NSIRRIAKNV F LHLHNLDL ...String:
MGNSGQFLDA AKALQVWPLI EKRTCWHGHA GGGLHTDPKE GLKDVDTRKI IKAMLSYVWP KDRPDLRARV AISLGFLGGA KAMNIVVPF MFKYAVDSLN QMSGNMLNLS DAPNTVATMA TAVLIGYGVS RAGAAFFNEV RNAVFGKVAQ NSIRRIAKNV F LHLHNLDL GFHLSRQTGA LSKAIDRGTR GISFVLSALV FNLLPIMFEV MLVSGVLYYK CGAQFALVTL GTLGTYTAFT VA VTRWRTR FRIEMNKADN DAGNAAIDSL LNYETVKYFN NERYEAQRYD GFLKTYETAS LKSTSTLAML NFGQSAIFSV GLT AIMVLA SQGIVAGTLT VGDLVMVNGL LFQLSLPLNF LGTVYRETRQ ALIDMNTLFT LLKVDTQIKD KVMASPLQIT PQTA TVAFD NVHFEYIEGQ KVLSGISFEV PAGKKVAIVG GSGSGKSTIV RLLFRFYEPQ KGSIYLAGQN IQDVSLESLR RAVGV VPQD AVLFHNTIYY NLLYGNISAS PEEVYAVAKL AGLHDAILRM PHGYDTQVGE RGLKLSGGEK QRVAIARAIL KDPPVI LYD EATSSLDSIT EETILGAMKD VVKHRTSIFI AHRLSTVVDA DEIIVLDQGK VAERGTHHGL LANPHSIYSE MWHTQSS RV QNHDNPKWEA KKENISKEEE RKKLQEEIVN SVKGCGNCSD YKDDDDKDYK DDDDK

UniProtKB: Iron-sulfur clusters transporter ABCB7, mitochondrial

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / 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

Concentration14 mg/mL
BufferpH: 6.5 / Details: 1 mM MgCl2 and 5 mM AMP-PNP
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
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:

7d7r

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 39927
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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