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Yorodumi- EMDB-23932: Cryo-EM structure of the yeast cadmium factor 1 protein (Ycf1p) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23932 | ||||||||||||
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Title | Cryo-EM structure of the yeast cadmium factor 1 protein (Ycf1p) | ||||||||||||
Map data | Endogenously expressed Ycf1p. Non-uniform refinement. | ||||||||||||
Sample |
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Keywords | ATP binding cassette (ABC) transporter / transmembrane domain 0 (TMD0) / regulatory (R) region / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Atorvastatin ADME / Paracetamol ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport ...ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Atorvastatin ADME / Paracetamol ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / vacuole fusion, non-autophagic / ABC-family proteins mediated transport / response to metal ion / fungal-type vacuole membrane / ATPase-coupled transmembrane transporter activity / response to cadmium ion / glutathione metabolic process / cell redox homeostasis / transmembrane transport / membrane raft / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Bickers SC / Benlekbir S / Rubinstein JL / Kanelis V | ||||||||||||
Funding support | Canada, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters. Authors: Sarah C Bickers / Samir Benlekbir / John L Rubinstein / Voula Kanelis / Abstract: ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two ...ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. While TMD0 was resolved in SUR1, the atypical ABCC protein that is part of the hetero-octameric ATP-sensitive K channel, little is known about the structure of TMD0 in monomeric ABC transporters. Here, we present the structure of yeast cadmium factor 1 protein (Ycf1p), a homolog of human MRP1, determined by electron cryo-microscopy (cryo-EM). A comparison of Ycf1p, SUR1, and a structure of MRP1 that showed TMD0 at low resolution demonstrates that TMD0 can adopt different orientations relative to the ABC core, including a ∼145° rotation between Ycf1p and SUR1. The cryo-EM map also reveals that segments of the regulatory (R) region, which links NBD1 to TMD2 and was poorly resolved in earlier ABCC structures, interacts with the L0 linker, NBD1, and TMD2. These interactions, combined with fluorescence quenching experiments of isolated NBD1 with and without the R region, suggest how posttranslational modifications of the R region modulate ABC protein activity. Mapping known mutations from MRP2 and MRP6 onto the Ycf1p structure explains how mutations involving TMD0 and the R region of these proteins lead to disease. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23932.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-23932-v30.xml emd-23932.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_23932.png | 52.1 KB | ||
Filedesc metadata | emd-23932.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23932 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23932 | HTTPS FTP |
-Validation report
Summary document | emd_23932_validation.pdf.gz | 362.1 KB | Display | EMDB validaton report |
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Full document | emd_23932_full_validation.pdf.gz | 361.7 KB | Display | |
Data in XML | emd_23932_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_23932_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23932 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23932 | HTTPS FTP |
-Related structure data
Related structure data | 7mpeMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23932.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Endogenously expressed Ycf1p. Non-uniform refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yeast cadmium factor 1 protein (Ycf1p)
Entire | Name: Yeast cadmium factor 1 protein (Ycf1p) |
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Components |
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-Supramolecule #1: Yeast cadmium factor 1 protein (Ycf1p)
Supramolecule | Name: Yeast cadmium factor 1 protein (Ycf1p) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: Endogenously expressed Ycf1p that also contains a C-terminal 3x FLAG tag. |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ2168 / Location in cell: Vacoular Membrane |
Molecular weight | Theoretical: 171.136 KDa |
-Macromolecule #1: Metal resistance protein YCF1
Macromolecule | Name: Metal resistance protein YCF1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type Cd2+ transporter |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ2168 |
Molecular weight | Theoretical: 174.024141 KDa |
Sequence | String: MAGNLVSWAC KLCRSPEGFG PISFYGDFTQ CFIDGVILNL SAIFMITFGI RDLVNLCKKK HSGIKYRRNW IIVSRMALVL LEIAFVSLA SLNISKEEAE NFTIVSQYAS TMLSLFVALA LHWIEYDRSV VANTVLLFYW LFETFGNFAK LINILIRHTY E GIWYSGQT ...String: MAGNLVSWAC KLCRSPEGFG PISFYGDFTQ CFIDGVILNL SAIFMITFGI RDLVNLCKKK HSGIKYRRNW IIVSRMALVL LEIAFVSLA SLNISKEEAE NFTIVSQYAS TMLSLFVALA LHWIEYDRSV VANTVLLFYW LFETFGNFAK LINILIRHTY E GIWYSGQT GFILTLFQVI TCASILLLEA LPKKPLMPHQ HIHQTLTRRK PNPYDSANIF SRITFSWMSG LMKTGYEKYL VE ADLYKLP RNFSSEELSQ KLEKNWENEL KQKSNPSLSW AICRTFGSKM LLAAFFKAIH DVLAFTQPQL LRILIKFVTD YNS ERQDDH SSLQGFENNH PQKLPIVRGF LIAFAMFLVG FTQTSVLHQY FLNVFNTGMY IKSALTALIY QKSLVLSNEA SGLS STGDI VNLMSVDVQK LQDLTQWLNL IWSGPFQIII CLYSLYKLLG NSMWVGVIIL VIMMPLNSFL MRIQKKLQKS QMKYK DERT RVISEILNNI KSLKLYAWEK PYREKLEEVR NNKELKNLTK LGCYMAVTSF QFNIVPFLVS CCTFAVFVYT EDRALT TDL VFPALTLFNL LSFPLMIIPM VLNSFIEASV SIGRLFTFFT NEELQPDSVQ RLPKVKNIGD VAINIGDDAT FLWQRKP EY KVALKNINFQ AKKGNLTCIV GKVGSGKTAL LSCMLGDLFR VKGFATVHGS VAYVSQVPWI MNGTVKENIL FGHRYDAE F YEKTIKACAL TIDLAILMDG DKTLVGEKGI SLSGGQKARL SLARAVYARA DTYLLDDPLA AVDEHVARHL IEHVLGPNG LLHTKTKVLA TNKVSALSIA DSIALLDNGE ITQQGTYDEI TKDADSPLWK LLNNYGKKNN GKSNEFGDSS ESSVRESSIP VEGELEQLQ KLNDLDFGNS DAISLRRASD ATLGSIDFGD DENIAKREHR EQGKVKWNIY LEYAKACNPK SVCVFILFIV I SMFLSVMG NVWLKHWSEV NSRYGSNPNA ARYLAIYFAL GIGSALATLI QTIVLWVFCT IHASKYLHNL MTNSVLRAPM TF FETTPIG RILNRFSNDI YKVDALLGRT FSQFFVNAVK VTFTITVICA TTWQFIFIII PLSVFYIYYQ QYYLRTSREL RRL DSITRS PIYSHFQETL GGLATVRGYS QQKRFSHINQ CRIDNNMSAF YPSINANRWL AYRLELIGSI IILGAATLSV FRLK QGTLT AGMVGLSLSY ALQITQTLNW IVRMTVEVET NIVSVERIKE YADLKSEAPL IVEGHRPPKE WPSQGDIKFN NYSTR YRPE LDLVLKHINI HIKPNEKVGI VGRTGAGKSS LTLALFRMIE ASEGNIVIDN IAINEIGLYD LRHKLSIIPQ DSQVFE GTV RENIDPINQY TDEAIWRALE LSHLKEHVLS MSNDGLDAQL TEGGGNLSVG QRQLLCLARA MLVPSKILVL DEATAAV DV ETDKVVQETI RTAFKDRTIL TIAHRLNTIM DSDRIIVLDN GKVAEFDSPG QLLSDNKSLF YSLCMEAGLV NENDYKDH D GDYKDHDIDY KDDDDK UniProtKB: Metal resistance protein YCF1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.5 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: Buffer was at 4 degrees Celsius. | ||||||||||||
Grid | Model: Homemade / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I | ||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 9.6 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |