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- EMDB-33603: Cryo-EM Structure of biliverdin-bound mitochondrial ABC transport... -

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Basic information

Entry
Database: EMDB / ID: EMD-33603
TitleCryo-EM Structure of biliverdin-bound mitochondrial ABC transporter ABCB10 from Biortus
Map datasharpened map
Sample
  • Complex: Complex of ABCB10 binding with biliverdin
    • Protein or peptide: ATP-binding cassette sub-family B member 10, mitochondrial
  • Ligand: CHOLESTEROL
  • Ligand: Biliverdine IX Alpha
KeywordsABC transporter / biliverdin / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of heme biosynthetic process / mitochondrial unfolded protein response / Mitochondrial ABC transporters / positive regulation of hemoglobin biosynthetic process / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane ...positive regulation of heme biosynthetic process / mitochondrial unfolded protein response / Mitochondrial ABC transporters / positive regulation of hemoglobin biosynthetic process / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP 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
ATP-binding cassette sub-family B member 10, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsCao S / Yang Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of mitochondrial ABC transporter ABCB10 in apo and biliverdin-bound form.
Authors: Sheng Cao / Yihu Yang / Lili He / Yumo Hang / Xiaodong Yan / Hui Shi / Jiaquan Wu / Zhuqing Ouyang /
Abstract: ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron ...ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron transporter mitoferrin-1. Recently, it was found that ABCB10 is a mitochondrial biliverdin exporter. However, the molecular mechanism of biliverdin export by ABCB10 remains elusive. Here we report the cryo-EM structures of ABCB10 in apo (ABCB10-apo) and biliverdin-bound form (ABCB10-BV) at 3.67 Å and 2.85 Å resolution, respectively. ABCB10-apo adopts a wide-open conformation and may thus represent the apo form structure. ABCB10-BV forms a closed conformation and biliverdin situates in a hydrophobic pocket in one protomer and bridges the interaction through hydrogen bonds with the opposing one. We also identify cholesterols sandwiched by BVs and discuss the export dynamics based on these structural and biochemical observations.
History
DepositionJun 14, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33603.png

Downloads & links

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Map

FileDownload / File: emd_33603.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.064996004 - 1.8214958
Average (Standard dev.)0.00056161836 (±0.015809607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33603_msk_1.map
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Additional map: original map

Fileemd_33603_additional_1.map
Annotationoriginal map
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Half map: #2

Fileemd_33603_half_map_1.map
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Half map: #1

Fileemd_33603_half_map_2.map
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Sample components

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Entire : Complex of ABCB10 binding with biliverdin

EntireName: Complex of ABCB10 binding with biliverdin
Components
  • Complex: Complex of ABCB10 binding with biliverdin
    • Protein or peptide: ATP-binding cassette sub-family B member 10, mitochondrial
  • Ligand: CHOLESTEROL
  • Ligand: Biliverdine IX Alpha

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Supramolecule #1: Complex of ABCB10 binding with biliverdin

SupramoleculeName: Complex of ABCB10 binding with biliverdin / type: complex / 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 10, mitochondrial

MacromoleculeName: ATP-binding cassette sub-family B member 10, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.180125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGLPEARKL LGLAYPERRR LAAAVGFLTM SSVISMSAPF FLGKIIDVIY TNPTVDYSDN LTRLCLGLSA VFLCGAAANA IRVYLMQTS GQRIVNRLRT SLFSSILRQE VAFFDKTRTG ELINRLSSDT ALLGRSVTEN LSDGLRAGAQ ASVGISMMFF V SPNLATFV ...String:
MAGLPEARKL LGLAYPERRR LAAAVGFLTM SSVISMSAPF FLGKIIDVIY TNPTVDYSDN LTRLCLGLSA VFLCGAAANA IRVYLMQTS GQRIVNRLRT SLFSSILRQE VAFFDKTRTG ELINRLSSDT ALLGRSVTEN LSDGLRAGAQ ASVGISMMFF V SPNLATFV LSVVPPVSII AVIYGRYLRK LTKVTQDSLA QATQLAEERI GNVRTVRAFG KEMTEIEKYA SKVDHVMQLA RK EAFARAG FFGATGLSGN LIVLSVLYKG GLLMGSAHMT VGELSSFLMY AFWVGISIGG LSSFYSELMK GLGAGGRLWE LLE REPKLP FNEGVILNEK SFQGALEFKN VHFAYPARPE VPIFQDFSLS IPSGSVTALV GPSGSGKSTV LSLLLRLYDP ASGT ISLDG HDIRQLNPVW LRSKIGTVSQ EPILFSCSIA ENIAYGADDP SSVTAEEIQR VAEVANAVAF IRNFPQGFNT VVGEK GVLL SGGQKQRIAI ARALLKNPKI LLLDQATSAL DAENEYLVQE ALDRLMDGRT VLVIAHRLST IKNANMVAVL DQGKIT EYG KHEELLSKPN GIYRKLMNKQ SFISAENLYF QGDYKDDDDK HHHHHHHHHH

UniProtKB: ATP-binding cassette sub-family B member 10, mitochondrial

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: Biliverdine IX Alpha

MacromoleculeName: Biliverdine IX Alpha / type: ligand / ID: 3 / Number of copies: 1 / Formula: IE5
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

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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

Concentration4.78 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa / Details: 5W
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.5 sec. / Average electron dose: 55.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
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:

4ayx

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206922
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4ayx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL / Overall B value: 97.3
Output model

PDB-7y48:
Cryo-EM Structure of biliverdin-bound mitochondrial ABC transporter ABCB10 from Biortus

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