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Yorodumi- EMDB-31487: Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31487 | |||||||||
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Title | Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with beryllium fluoride (resting state) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | P4-ATPases / LIPID TRANSPORT | |||||||||
Function / homology | Function and homology information regulation of vacuole organization / aminophospholipid translocation / phospholipid-translocating ATPase complex / phospholipid translocation / cell surface receptor signaling pathway / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.81 Å | |||||||||
Authors | Xu J / He Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Rep / Year: 2022 Title: Conformational changes of a phosphatidylcholine flippase in lipid membranes. Authors: Jinkun Xu / Yilin He / Xiaofei Wu / Long Li / Abstract: Type 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid ...Type 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid flipping. It is unclear how the active flipping states of P4-ATPases are regulated in the lipid membranes, especially for phosphatidylcholine (PC)-flipping P4-ATPases whose substrate, PC, is a substantial component of membranes. Here, we report the cryoelectron microscopy structures of a yeast PC-flipping P4-ATPase, Dnf1, in lipid environments. In native yeast lipids, Dnf1 adopts a conformation in which the lipid flipping pathway is disrupted. Only when the lipid composition is changed can Dnf1 be captured in the active conformations that enable lipid flipping. These results suggest that, in the native membrane, Dnf1 may stay in an idle conformation that is unable to support the trans-membrane movement of lipids. Dnf1 may have altered conformational preferences in membranes with different lipid compositions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31487.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-31487-v30.xml emd-31487.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_31487.png | 129.3 KB | ||
Filedesc metadata | emd-31487.cif.gz | 6.7 KB | ||
Others | emd_31487_additional_1.map.gz | 69.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31487 | HTTPS FTP |
-Validation report
Summary document | emd_31487_validation.pdf.gz | 351.8 KB | Display | EMDB validaton report |
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Full document | emd_31487_full_validation.pdf.gz | 351.4 KB | Display | |
Data in XML | emd_31487_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_31487_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31487 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31487 | HTTPS FTP |
-Related structure data
Related structure data | 7f7fMC 7drxC 7dshC 7dsiC 7whvC 7whwC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31487.map.gz / Format: CCP4 / Size: 103 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: 1.055 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_31487_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dnf1_Lem3 complex
Entire | Name: Dnf1_Lem3 complex |
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Components |
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-Supramolecule #1: Dnf1_Lem3 complex
Supramolecule | Name: Dnf1_Lem3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
-Macromolecule #1: Phospholipid-transporting ATPase DNF1
Macromolecule | Name: Phospholipid-transporting ATPase DNF1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 178.000172 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae S288C (yeast) |
Sequence | String: MSGTFHGDGH APMSPFEDTF QFEDNSSNED THIAPTHFDD GATSNKYSRP QVSFNDETPK NKREDAEEFT FNDDTEYDNH SFQPTPKLN NGSGTFDDVE LDNDSGEPHT NYDGMKRFRM GTKRNKKGNP IMGRSKTLKW ARKNIPNPFE DFTKDDIDPG A INRAQELR ...String: MSGTFHGDGH APMSPFEDTF QFEDNSSNED THIAPTHFDD GATSNKYSRP QVSFNDETPK NKREDAEEFT FNDDTEYDNH SFQPTPKLN NGSGTFDDVE LDNDSGEPHT NYDGMKRFRM GTKRNKKGNP IMGRSKTLKW ARKNIPNPFE DFTKDDIDPG A INRAQELR TVYYNMPLPK DMIDEEGNPI MQYPRNKIRT TKYTPLTFLP KNILFQFHNF ANVYFLVLII LGAFQIFGVT NP GLSAVPL VVIVIITAIK DAIEDSRRTV LDLEVNNTKT HILEGVENEN VSTDNISLWR RFKKANSRLL FKFIQYCKEH LTE EGKKKR MQRKRHELRV QKTVGTSGPR SSLDSIDSYR VSADYGRPSL DYDNLEQGAG EANIVDRSLP PRTDCKFAKN YWKG VKVGD IVRIHNNDEI PADIILLSTS DTDGACYVET KNLDGETNLK VRQSLKCTNT IRTSKDIART KFWIESEGPH SNLYT YQGN MKWRNLADGE IRNEPITINN VLLRGCTLRN TKWAMGVVMF TGGDTKIMLN SGITPTKKSR ISRELNFSVV INFVLL FIL CFVSGIANGV YYDKKGRSRF SYEFGTIAGS AATNGFVSFW VAVILYQSLV PISLYISVEI IKTAQAAFIY GDVLLYN AK LDYPCTPKSW NISDDLGQVE YIFSDKTGTL TQNVMEFKKC TINGVSYGRA YTEALAGLRK RQGIDVETEG RREKAEIA K DRDTMIDELR ALSGNSQFYP EEVTFVSKEF VRDLKGASGE VQQRCCEHFM LALALCHSVL VEANPDNPKK LDLKAQSPD EAALVATARD VGFSFVGKTK KGLIIEMQGI QKEFEILNIL EFNSSRKRMS CIVKIPGLNP GDEPRALLIC KGADSIIYSR LSRQSGSNS EAILEKTALH LEQYATEGLR TLCIAQRELS WSEYEKWNEK YDIAAASLAN REDELEVVAD SIERELILLG G TAIEDRLQ DGVPDCIELL AEAGIKLWVL TGDKVETAIN IGFSCNLLNN EMELLVIKTT GDDVKEFGSE PSEIVDALLS KY LKEYFNL TGSEEEIFEA KKDHEFPKGN YAIVIDGDAL KLALYGEDIR RKFLLLCKNC RAVLCCRVSP SQKAAVVKLV KDS LDVMTL AIGDGSNDVA MIQSADVGIG IAGEEGRQAV MCSDYAIGQF RYLARLVLVH GRWSYKRLAE MIPEFFYKNM IFAL ALFWY GIYNDFDGSY LYEYTYMMFY NLAFTSLPVI FLGILDQDVN DTISLVVPQL YRVGILRKEW NQRKFLWYML DGLYQ SIIC FFFPYLVYHK NMIVTSNGLG LDHRYFVGVY VTTIAVISCN TYVLLHQYRW DWFSGLFIAL SCLVVFAWTG IWSSAI ASR EFFKAAARIY GAPSFWAVFF VAVLFCLLPR FTYDSFQKFF YPTDVEIVRE MWQHGHFDHY PPGYDPTDPN RPKVTKA GQ HGEKIIEGIA LSDNLGGSNY SRDSVVTEEI PMTFMHGEDG SPSGYQKQET WMTSPKETQD LLQSPQFQQA QTFGRGPS T NVRSSLDRTR EQMIATNQLD NRYSVERART SLDLPGVTNA ASLIGTQQNN UniProtKB: UNIPROTKB: P32660 |
-Macromolecule #2: Alkylphosphocholine resistance protein LEM3
Macromolecule | Name: Alkylphosphocholine resistance protein LEM3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 47.490395 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae S288C (yeast) |
Sequence | String: MVNFDLGQVG EVFRRKDKGA IVSGDNPEEE EDVDASEFEE DEVKPVRTKN RRPKEDAFTQ QRLAAINPVL TPRTVLPLYL LIAVVFVIV GGCILAQNSK VDEVTIYYQD CMTNATSSWS DIPSEHWQFV FHKYKTYNTA PQWRFVDDES DDFTKQRGTC Q IRFTTPSD ...String: MVNFDLGQVG EVFRRKDKGA IVSGDNPEEE EDVDASEFEE DEVKPVRTKN RRPKEDAFTQ QRLAAINPVL TPRTVLPLYL LIAVVFVIV GGCILAQNSK VDEVTIYYQD CMTNATSSWS DIPSEHWQFV FHKYKTYNTA PQWRFVDDES DDFTKQRGTC Q IRFTTPSD MKNNVYLNYV LEKFAANHRR YVLSFSEDQI RGEDASYETV HDATGINCKP LSKNADGKIY YPCGLIANSM FN DTFPLQL TNVGDTSNNY SLTNKGINWE SDKKRYKKTK YNYTQIAPPP YWEKMYPDGY NETNIPDIQD WEEFQNWMRP GAF DKITKL IRINKNDTLP AGEYQLDIGL HWPVLEFNGK KGIYLTHGSH LGGRNPFLGI VYLIGGCICA AMALILLTFW LFGG RKIAD ASSLSWNMK UniProtKB: Phospholipid-transporting ATPase accessory subunit LEM3 |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212294 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: RANDOM ASSIGNMENT |