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- EMDB-63057: bovine ABCC1 bound to estrogen sulfate and GSH -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63057
Titlebovine ABCC1 bound to estrogen sulfate and GSH
Map data
Sample
  • Complex: inward-open bABCC1 bound to E1SO4 and GSH
    • Protein or peptide: Multidrug resistance-associated protein 1
  • Ligand: estrone 3-sulfate
  • Ligand: GLUTATHIONE
KeywordsABC transporter / inward-open ABCC1 / estrogen sulfate / GSH / PROTEIN TRANSPORT
Function / homology
Function and homology information


Sphingolipid de novo biosynthesis / Heme degradation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / Transport of RCbl within the body / cyclic nucleotide transport / Paracetamol ADME / ABC-family proteins mediated transport / glutathione transmembrane transport / leukotriene transport / ABC-type glutathione S-conjugate transporter activity ...Sphingolipid de novo biosynthesis / Heme degradation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / Transport of RCbl within the body / cyclic nucleotide transport / Paracetamol ADME / ABC-family proteins mediated transport / glutathione transmembrane transport / leukotriene transport / ABC-type glutathione S-conjugate transporter activity / glutathione transmembrane transporter activity / Cytoprotection by HMOX1 / ABC-type glutathione-S-conjugate transporter / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / xenobiotic transport / lipid transport / xenobiotic transmembrane transporter activity / ABC-type transporter activity / positive regulation of inflammatory response / basolateral plasma membrane / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding
Similarity search - Function
Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / 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. ...Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / 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
Multidrug resistance-associated protein 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsSun PP / Liu KX / Gao P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: bovine ABCC1 bound to estrogen sulfate and GSH
Authors: Sun PP / Liu KX / Gao P
History
DepositionJan 10, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63057.png

Downloads & links

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Map

FileDownload / File: emd_63057.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-0.6798703 - 1.0929371
Average (Standard dev.)-0.00057213614 (±0.020088993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63057_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63057_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : inward-open bABCC1 bound to E1SO4 and GSH

EntireName: inward-open bABCC1 bound to E1SO4 and GSH
Components
  • Complex: inward-open bABCC1 bound to E1SO4 and GSH
    • Protein or peptide: Multidrug resistance-associated protein 1
  • Ligand: estrone 3-sulfate
  • Ligand: GLUTATHIONE

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Supramolecule #1: inward-open bABCC1 bound to E1SO4 and GSH

SupramoleculeName: inward-open bABCC1 bound to E1SO4 and GSH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Multidrug resistance-associated protein 1

MacromoleculeName: Multidrug resistance-associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type xenobiotic transporter
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 175.004688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALRDFCSVD GSDLFWEWNV TWNTSNPDFT KCFQNTVLVW VPCSYLWVCF PFYFLYLSHH DRGYIQMTHL NKAKTALGFL LWIVCWADL FYSFWERSMG KLLAPVFLVS PTLLGITMLL ATFLIQIERR RGVQSSGIML TFWLIALLCA LAILRSKIMT A LKEDARVD ...String:
MALRDFCSVD GSDLFWEWNV TWNTSNPDFT KCFQNTVLVW VPCSYLWVCF PFYFLYLSHH DRGYIQMTHL NKAKTALGFL LWIVCWADL FYSFWERSMG KLLAPVFLVS PTLLGITMLL ATFLIQIERR RGVQSSGIML TFWLIALLCA LAILRSKIMT A LKEDARVD VFRDVTFYIY FSLVLIQLVL SCFSDRSPLF SETINDPNPC PESSASFLSR ITFWWITGMM VQGYRQPLES TD LWSLNKE DTSEQVVPVL VKNWKKECAK SRKQPVKIVY SSKDPAKPKG SSKVDVNEEA EALIVKCPQK ERDPSLFKVL YKT FGPYFL MSFLFKAVHD LMMFAGPEIL KLLINFVNDK KAPEWQGYFY TALLFISACL QTLVLHQYFH ICFVSGMRIK TAVI GAVYR KALVITNAAR KSSTVGEIVN LMSVDAQRFM DLATYINMIW SAPLQVILAL YLLWLNLGPS VLAGVAVMVL MVPLN AVMA MKTKTYQVAH MKSKDNRIKL MNEILNGIKV LKLYAWELAF KDKVLAIRQE ELKVLKKSAY LAAVGTFTWV CTPFLV ALS TFAVYVTVDE NNILDAQKAF VSLALFNILR FPLNILPMVI SSIVQASVSL KRLRVFLSHE DLDPDSIQRR PIKDAGA TN SITVKNATFT WARNDPPTLH GITFSVPEGS LVAVVGQVGC GKSSLLSALL AEMDKVEGHV TVKGSVAYVP QQAWIQNI S LRENILFGRQ LQERYYKAVV EACALLPDLE ILPSGDRTEI GEKGVNLSGG QKQRVSLARA VYCDSDVYLL DDPLSAVDA HVGKHIFENV IGPKGLLKNK TRLLVTHAIS YLPQMDVIIV MSGGKISEMG SYQELLARDG AFAEFLRTYA SAEQEQGQPE DGLAGVGGP GKEVKQMENG MLVTDTAGKQ MQRQLSSSSS YSRDVSQHHT STAELRKPGP TEETWKLVEA DKAQTGQVKL S VYWDYMKA IGLFISFLSI FLFLCNHVAS LVSNYWLSLW TDDPIVNGTQ EHTQVRLSVY GALGISQGIT VFGYSMAVSI GG IFASRRL HLDLLHNVLR SPISFFERTP SGNLVNRFSK ELDTVDSMIP QVIKMFMGSL FNVIGACIII LLATPMAAVI IPP LGLIYF FVQRFYVASS RQLKRLESVS RSPVYSHFNE TLLGVSVIRA FEEQERFIRQ SDLKVDENQK AYYPSIVANR WLAV RLECV GNCIVLFASL FAVISRHSLS AGLVGLSVSY SLQVTTYLNW LVRMSSEMET NIVAVERLKE YSETEKEAPW QIQDM APPK DWPQVGRVEF RDYGLRYRED LDLVLKHINV TIDGGEKVGI VGRTGAGKSS LTLGLFRIKE SAEGEIIIDD INIAKI GLH DLRFKITIIP QDPVLFSGSL RMNLDPFSQY SDEEVWTSLE LAHLKGFVSA LPDKLNHECA EGGENLSVGQ RQLVCLA RA LLRKTKILVL DEATAAVDLE TDDLIQSTIR TQFDDCTVLT IAHRLNTIMD YTRVIVLDKG EIQEWGSPSD LLQQRGLF Y SMAKDSGLVK LGSENLYFQG GSGGSGHHHH HHHHHHH

UniProtKB: Multidrug resistance-associated protein 1

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Macromolecule #2: estrone 3-sulfate

MacromoleculeName: estrone 3-sulfate / type: ligand / ID: 2 / Number of copies: 1 / Formula: FY5
Molecular weightTheoretical: 350.429 Da
Chemical component information

ChemComp-FY5:
estrone 3-sulfate

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Macromolecule #3: GLUTATHIONE

MacromoleculeName: GLUTATHIONE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GSH
Molecular weightTheoretical: 307.323 Da
Chemical component information

ChemComp-GSH:
GLUTATHIONE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111086
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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