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Yorodumi- EMDB-14757: ABCB1 L335C mutant (mABCB1) in the inward facing state bound to AAC -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14757 | |||||||||
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Title | ABCB1 L335C mutant (mABCB1) in the inward facing state bound to AAC | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / cellular response to external biotic stimulus ...hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / cellular response to external biotic stimulus / regulation of intestinal absorption / negative regulation of sensory perception of pain / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / response to alcohol / terpenoid transport / ceramide floppase activity / response to glycoside / ceramide translocation / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / ABC-family proteins mediated transport / phosphatidylethanolamine flippase activity / response to thyroxine / phosphatidylcholine floppase activity / establishment of blood-brain barrier / xenobiotic transport across blood-brain barrier / export across plasma membrane / ABC-type xenobiotic transporter / xenobiotic detoxification by transmembrane export across the plasma membrane / cellular response to L-glutamate / intercellular canaliculus / P-type phospholipid transporter / response to vitamin D / ABC-type xenobiotic transporter activity / response to vitamin A / intestinal absorption / response to glucagon / phospholipid translocation / cellular response to antibiotic / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / cellular response to estradiol stimulus / response to progesterone / female pregnancy / brush border membrane / placenta development / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Parey K / Januliene D / Gewering T / Moeller A / Vecchis D / Striednig B / Hilbi H / Schaefer LV / Kuprov I / Bordignon E / Seeger MA | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: To Be Published Title: ABCB1 L335C mutant (mABCB1) in the inward facing state bound to AAC Authors: Gewering T / Waghray D / Parey K / Januliene D / Urbatsch I / Moeller A / Zhang Q | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14757.map.gz | 79 MB | EMDB map data format | |
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Header (meta data) | emd-14757-v30.xml emd-14757.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14757_fsc.xml | 9.7 KB | Display | FSC data file |
Images | emd_14757.png | 78.3 KB | ||
Masks | emd_14757_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-14757.cif.gz | 6.8 KB | ||
Others | emd_14757_additional_1.map.gz emd_14757_additional_2.map.gz emd_14757_half_map_1.map.gz emd_14757_half_map_2.map.gz | 77.9 MB 41.3 MB 77.8 MB 77.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14757 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14757 | HTTPS FTP |
-Validation report
Summary document | emd_14757_validation.pdf.gz | 886.4 KB | Display | EMDB validaton report |
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Full document | emd_14757_full_validation.pdf.gz | 886 KB | Display | |
Data in XML | emd_14757_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_14757_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14757 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14757 | HTTPS FTP |
-Related structure data
Related structure data | 7zk7 M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14757.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14757_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: density modified map
File | emd_14757_additional_1.map | ||||||||||||
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Annotation | density modified map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_14757_additional_2.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14757_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14757_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ABCB1
Entire | Name: ABCB1 |
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Components |
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-Supramolecule #1: ABCB1
Supramolecule | Name: ABCB1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 140 kDa/nm |
-Macromolecule #1: ATP-dependent translocase ABCB1
Macromolecule | Name: ATP-dependent translocase ABCB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type xenobiotic transporter |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 146.063859 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MELEEDLKGR ADKNFSKMGK KSKKEKKEKK PAVSVLTMFR YAGWLDRLYM LVGTLAAIIH GVALPLMMLI FGDMTDSFAS VGQVSKQST QMSEADKRAM FAKLEEEMTT YAYYYTGIGA GVLIVAYIQV SFWALAAGRQ IHKIRQKFFH AIMNQEIGWF D VHDVGELN ...String: MELEEDLKGR ADKNFSKMGK KSKKEKKEKK PAVSVLTMFR YAGWLDRLYM LVGTLAAIIH GVALPLMMLI FGDMTDSFAS VGQVSKQST QMSEADKRAM FAKLEEEMTT YAYYYTGIGA GVLIVAYIQV SFWALAAGRQ IHKIRQKFFH AIMNQEIGWF D VHDVGELN TRLTDDVSKI NEGIGDKIGM FFQAMATFFG GFIIGFTRGW KLTLVILAIS PVLGLSAGIW AKILSSFTDK EL HAYAKAG AVAEEVLAAI RTVIAFGGQK KELERYNNNL EEAKRLGIKK AITANISMGA AFLLIYASYA LAFWYGTSLV ISK EYSIGQ VLTVFFSVCI GAFSVGQASP NIEAFANARG AAYEVFKIID NKPSIDSFSK SGHKPDNIQG NLEFKNIHFS YPSR KEVQI LKGLNLKVKS GQTVALVGNS GGGKSTTVQL MQRLYDPLDG MVSIDGQDIR TINVRYLREI IGVVSQEPVL FATTI AENI RYGREDVTMD EIEKAVKEAN AYDFIMKLPH QFDTLVGERG AQLSGGQKQR IAIARALVRN PKILLLDEAT SALDTE SEA VVQAALDKAR EGRTTIVIAH RLSTVRNADV IAGFDGGVIV EQGNHDELMR EKGIYFKLVM TQTAGNEIEL GNEAGKS KD EIDNLDMSSK DSGSSLIRRR STRKSITGPH DQDRKLSTKE ALDEDVPPAS FWRILKLNST EWPYFVVGIF AAIINGGL Q PAFSVIFSKV VGVFTNGGPP ETQRQNSNLF SLLFLILGII SFITFFLQGF TFGKAGEILT KRLRYMVFKS MLRQDVSWF DDPKNTTGAL TTRLANDAAQ VKGATGSRLA VIFQNIANLG TGIIISLIYG WQLTLLLLAI VPIIAIAGVV EMKMLSGQAL KDKKELEGS GKIATEAIEN FRTVVSLTRE QKFETMYAQS LQIPYRNAMK KAHVFGITFS FTQAMMYFSY AAAFRFGAYL V TQQLMTFE NVLLVFSAIV FGAMAVGQVS SFAPDYAKAT VSASHIIRII EKTPEIDSYS TQGLKPNMLE GNVQFSGVVF NY PTRPSIP VLQGLSLEVK KGQTLALVGS SGGGKSTVVQ LLERFYDPMA GSVFLDGKEI KQLNVQWLRA QLGIVSQEPI LFD RSIAEN IAYGDNSRVV SYEEIVRAAK EANIHQFIDS LPDKYNTRVG DKGTQLSGGQ KQRIAIARAL VRQPHILLLD EATS ALDTE SEKVVQEALD KAREGRTVIV IAHRLSTIQN ADLIVVIQNG KVKEHGTHQQ LLAQKGIYFS MVSVQAGAKR SLEEN LYFQ GGGASGGSWS HPQFEKAAAG GGSGGGSWSH PQFEKGSGHH HHHH UniProtKB: ATP-dependent translocase ABCB1 |
-Macromolecule #2: (4S,11S,18S)-4-[[(2,4-dinitrophenyl)disulfanyl]methyl]-11,18-dime...
Macromolecule | Name: (4S,11S,18S)-4-[[(2,4-dinitrophenyl)disulfanyl]methyl]-11,18-dimethyl-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione type: ligand / ID: 2 / Number of copies: 1 / Formula: JJI |
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Molecular weight | Theoretical: 692.79 Da |
Chemical component information | ChemComp-JJI: |
-Macromolecule #3: (4~{S},11~{S},18~{S})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-t...
Macromolecule | Name: (4~{S},11~{S},18~{S})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione type: ligand / ID: 3 / Number of copies: 1 / Formula: JIZ |
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Molecular weight | Theoretical: 494.634 Da |
Chemical component information | ChemComp-JIZ: |
-Macromolecule #4: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model |
PDB-7zk7: |