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- EMDB-31722: Cryo-EM structure of the mouse ABCB9 (ADP.BeF3-bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-31722
TitleCryo-EM structure of the mouse ABCB9 (ADP.BeF3-bound)
Map data
Sample
  • Cell: ABCB9
    • Protein or peptide: ABC-type oligopeptide transporter ABCB9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsABCB9 / peptide transporter / Lipid floppase / TAPL / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type oligopeptide transporter / ABC-type oligopeptide transporter activity / ABC-type peptide transporter activity / peptide metabolic process / ABC-family proteins mediated transport / peptide transport / ATPase-coupled transmembrane transporter activity / transmembrane transport / protein transport / lysosome ...ABC-type oligopeptide transporter / ABC-type oligopeptide transporter activity / ABC-type peptide transporter activity / peptide metabolic process / ABC-family proteins mediated transport / peptide transport / ATPase-coupled transmembrane transporter activity / transmembrane transport / protein transport / lysosome / lysosomal membrane / endoplasmic reticulum membrane / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ATP-binding cassette subfamily B member 9 / 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 subfamily B member 9 / 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
ABC-type oligopeptide transporter ABCB9
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPark JG / Kim S / Jang E / Choi SH / Han H / Kim JW / Ju S / Min DS / Jin MS
Funding support Korea, Republic Of, 4 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4022846 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1I1A1A01072077 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A6A3A13064599 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2022
Title: The lysosomal transporter TAPL has a dual role as peptide translocator and phosphatidylserine floppase.
Authors: Jun Gyou Park / Songwon Kim / Eunhong Jang / Seung Hun Choi / Hyunsu Han / Seulgi Ju / Ji Won Kim / Da Sol Min / Mi Sun Jin /
Abstract: TAPL is a lysosomal ATP-binding cassette transporter that translocates a broad spectrum of polypeptides from the cytoplasm into the lysosomal lumen. Here we report that, in addition to its well-known ...TAPL is a lysosomal ATP-binding cassette transporter that translocates a broad spectrum of polypeptides from the cytoplasm into the lysosomal lumen. Here we report that, in addition to its well-known role as a peptide translocator, TAPL exhibits an ATP-dependent phosphatidylserine floppase activity that is the possible cause of its high basal ATPase activity and of the lack of coupling between ATP hydrolysis and peptide efflux. We also present the cryo-EM structures of mouse TAPL complexed with (i) phospholipid, (ii) cholesteryl hemisuccinate (CHS) and 9-mer peptide, and (iii) ADP·BeF. The inward-facing structure reveals that F449 protrudes into the cylindrical transport pathway and divides it into a large hydrophilic central cavity and a sizable hydrophobic upper cavity. In the structure, the peptide binds to TAPL in horizontally-stretched fashion within the central cavity, while lipid molecules plug vertically into the upper cavity. Together, our results suggest that TAPL uses different mechanisms to function as a peptide translocase and a phosphatidylserine floppase.
History
DepositionAug 17, 2021-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31722.png

Downloads & links

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Map

FileDownload / File: emd_31722.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 260 pix.
= 215.8 Å		0.83 Å/pix.
x 260 pix.
= 215.8 Å		0.83 Å/pix.
x 260 pix.
= 215.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3132056 - 2.1341834
Average (Standard dev.)0.0031492913 (±0.07096988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 215.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ABCB9

EntireName: ABCB9
Components
  • Cell: ABCB9
    • Protein or peptide: ABC-type oligopeptide transporter ABCB9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ABCB9

SupramoleculeName: ABCB9 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: ABC-type oligopeptide transporter ABCB9

MacromoleculeName: ABC-type oligopeptide transporter ABCB9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type oligopeptide transporter
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 84.046805 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MRLWKAVVVT LAFVSTDVGV TTAIYAFSHL DRSLLEDIRH FNIFDSVLDL WAACLYRSCL LLGATIGVAK NSALGPRRLR ASWLVITLV CLFVGIYAMA KLLLFSEVRR PIRDPWFWAL FVWTYISLAA SFLLWGLLAT VRPDAEALEP GNEGFHGEGG A PAEQASGA ...String:
MRLWKAVVVT LAFVSTDVGV TTAIYAFSHL DRSLLEDIRH FNIFDSVLDL WAACLYRSCL LLGATIGVAK NSALGPRRLR ASWLVITLV CLFVGIYAMA KLLLFSEVRR PIRDPWFWAL FVWTYISLAA SFLLWGLLAT VRPDAEALEP GNEGFHGEGG A PAEQASGA TLQKLLSYTK PDVAFLVAAS FFLIVAALGE TFLPYYTGRA IDSIVIQKSM DQFTTAVVVV CLLAIGSSLA AG IRGGIFT LVFARLNIRL RNCLFRSLVS QETSFFDENR TGDLISRLTS DTTMVSDLVS QNINIFLRNT VKVTGVVVFM FSL SWQLSL VTFMGFPIIM MVSNIYGKYY KRLSKEVQSA LARASTTAEE TISAMKTVRS FANEEEEAEV FLRKLQQVYK LNRK EAAAY MSYVWGSGLT LLVVQVSILY YGGHLVISGQ MSSGNLIAFI IYEFVLGDCM ESVGSVYSGL MQGVGAAEKV FEFID RQPT MVHDGSLAPD HLEGRVDFEN VTFTYRTRPH TQVLQNVSFS LSPGKVTALV GPSGSGKSSC VNILENFYPL QGGRVL LDG KPIGAYDHKY LHRVISLVSQ EPVLFARSIT DNISYGLPTV PFEMVVEAAQ KANAHGFIME LQDGYSTETG EKGAQLS GG QKQRVAMARA LVRNPPVLIL DEATSALDAE SEYLIQQAIH GNLQRHTVLI IAHRLSTVER AHLIVVLDKG RVVQQGTH Q QLLAQGGLYA KLVQRQMLGL EHPLDYTASH KEPPSNTEHK A

UniProtKB: ABC-type oligopeptide transporter ABCB9

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3zdq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212390
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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