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- EMDB-46408: OATP1B1 Outward Facing with Atorvastatin -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-46408
TitleOATP1B1 Outward Facing with Atorvastatin
Map dataOATP1B1 Outward Facing with Atorvastatin
Sample
  • Organelle or cellular component: OATP1B1
    • Protein or peptide: OATP1B1
KeywordsOATP1B1 / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsSung M / Han S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: OATP1B1 identified in Outward Facing conformation in the presence of Atorvastatin resolved at 3.79 angstroms
Authors: Sung M / Han S / Lees J
History
DepositionAug 5, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46408.png

Downloads & links

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Map

FileDownload / File: emd_46408.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOATP1B1 Outward Facing with Atorvastatin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 180 pix.
= 263.88 Å		1.47 Å/pix.
x 180 pix.
= 263.88 Å		1.47 Å/pix.
x 180 pix.
= 263.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.466 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.0006653177 - 2.5616562
Average (Standard dev.)0.001959421 (±0.034358397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 263.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46408_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: OATP1B1 Outward Facing with Atorvastatin

Fileemd_46408_half_map_1.map
AnnotationOATP1B1 Outward Facing with Atorvastatin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: OATP1B1 Outward Facing with Atorvastatin

Fileemd_46408_half_map_2.map
AnnotationOATP1B1 Outward Facing with Atorvastatin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OATP1B1

EntireName: OATP1B1
Components
  • Organelle or cellular component: OATP1B1
    • Protein or peptide: OATP1B1

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Supramolecule #1: OATP1B1

SupramoleculeName: OATP1B1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: OATP1B1

MacromoleculeName: OATP1B1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: DQNQHLNKTA EAQPSENKKT RYCNGLKMFL AALSLSFIAK TLGAIIMKSS IIHIERRFEI SSSLVGFIDG SFEIGNLLVI VFVSYFGSKL HRPKLIGIGC FIMGIGGVLT ALPHFFMGYY RYSKETNINS SENSTSTLST CLINQILSLN RASPEIVGKG CLKESGSYMW ...String:
DQNQHLNKTA EAQPSENKKT RYCNGLKMFL AALSLSFIAK TLGAIIMKSS IIHIERRFEI SSSLVGFIDG SFEIGNLLVI VFVSYFGSKL HRPKLIGIGC FIMGIGGVLT ALPHFFMGYY RYSKETNINS SENSTSTLST CLINQILSLN RASPEIVGKG CLKESGSYMW IYVFMGNMLR GIGETPIVPL GLSYIDDFAK EGHSSLYLGI LNAIAMIGPI IGFTLGSLFS KMYVDIGYVD LSTIRITPTD SRWVGAWWLN FLVSGLFSII SSIPFFFLPQ TPNKPQKERK ASLSLHVLET NDEKDQTANL TNQGKNITKN VTGFFQSFKS ILTNPLYVMF VLLTLLQVSS YIGAFTYVFK YVEQQYGQPS SKANILLGVI TIPIFASGMF LGGYIIKKFK LNTVGIAKFS CFTAVMSLSF YLLYFFILCE NKSVAGLTMT YDGNNPVTSH RDVPLSYCNS DCNCDESQWE PVCGNNGITY ISPCLAGCKS SSGNKKPIVF YNCSCLEVTG LQNRNYSAHL GECPRDDACT RKFYFFVAIQ VLNLFFSALG GTSHVMLIVK IVQPELKSLA LGFHSMVIRA LGGILAPIYF GALIDTTCIK WSTNNCGTRG SCRTYNSTSF SRVYLGLSSM LRVSSLVLYI ILIYAMKKKY QEKDINASEN GSVMDEANLE SLNKNKHFVP SAGADSETHC

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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 TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83644
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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