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- EMDB-23072: Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23072 | |||||||||
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Title | Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state | |||||||||
![]() | Cryo-EM 3D map of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state | |||||||||
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Function / homology | ![]() regulation of vacuole organization / glycosylceramide flippase activity / mating projection tip membrane / aminophospholipid translocation / Ion transport by P-type ATPases / aminophospholipid flippase activity / phosphatidylserine flippase activity / ceramide translocation / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity ...regulation of vacuole organization / glycosylceramide flippase activity / mating projection tip membrane / aminophospholipid translocation / Ion transport by P-type ATPases / aminophospholipid flippase activity / phosphatidylserine flippase activity / ceramide translocation / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / cellular bud neck / P-type phospholipid transporter / phospholipid translocation / establishment or maintenance of cell polarity / cell periphery / endocytosis / protein transport / cell surface receptor signaling pathway / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.05 Å | |||||||||
![]() | Bai L / You Q / Jain BK / Duan HD / Kovach A / Graham TR / Li H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Transport mechanism of P4 ATPase phosphatidylcholine flippases. Authors: Lin Bai / Qinglong You / Bhawik K Jain / H Diessel Duan / Amanda Kovach / Todd R Graham / Huilin Li / ![]() ![]() Abstract: The P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases-such as the yeast Drs2 ...The P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases-such as the yeast Drs2 and human ATP8A1-have recently been reported. However, a substrate-binding site on the cytosolic side has not been found, and the transport mechanisms of P4 ATPases with other substrates are unknown. Here, we report structures of the Dnf1-Lem3 and Dnf2-Lem3 complexes. We captured substrate phosphatidylcholine molecules on both the exoplasmic and cytosolic sides and found that they have similar structures. Unexpectedly, Lem3 contributes to substrate binding. The conformational transitions of these phosphatidylcholine transporters match those of the phosphatidylserine transporters, suggesting a conserved mechanism among P4 ATPases. Dnf1/Dnf2 have a unique P domain helix-turn-helix insertion that is important for function. Therefore, P4 ATPases may have retained an overall transport mechanism while evolving distinct features for different lipid substrates. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
Images | ![]() | 51.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ky9MC ![]() 7ky5C ![]() 7ky6C ![]() 7ky7C ![]() 7ky8C ![]() 7kyaC ![]() 7kybC ![]() 7kycC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM 3D map of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in t...
Entire | Name: S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state |
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Components |
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-Supramolecule #1: S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in t...
Supramolecule | Name: S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ADP state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Recombinant expression | Organism: ![]() ![]() Recombinant strain: ATCC 204508 / S288c |
-Macromolecule #1: Phospholipid-transporting ATPase DNF2
Macromolecule | Name: Phospholipid-transporting ATPase DNF2 / 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: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 182.834469 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSSPSKPTSP FVDDIEHESG SASNGLSSMS PFDDSFQFEK PSSAHGNIEV AKTGGSVLKR QSKPMKDIST PDLSKVTFDG IDDYSNDND INDDDELNGK KTEIHEHENE VDDDLHSFQA TPMPNTGGFE DVELDNNEGS NNDSQADHKL KRVRFGTRRN K SGRIDINR ...String: MSSPSKPTSP FVDDIEHESG SASNGLSSMS PFDDSFQFEK PSSAHGNIEV AKTGGSVLKR QSKPMKDIST PDLSKVTFDG IDDYSNDND INDDDELNGK KTEIHEHENE VDDDLHSFQA TPMPNTGGFE DVELDNNEGS NNDSQADHKL KRVRFGTRRN K SGRIDINR SKTLKWAKKN FHNAIDEFST KEDSLENSAL QNRSDELRTV YYNLPLPEDM LDEDGLPLAV YPRNKIRTTK YT PLTFFPK NILFQFHNFA NIYFLILLIL GAFQIFGVTN PGFASVPLIV IVIITAIKDG IEDSRRTVLD LEVNNTRTHI LSG VKNENV AVDNVSLWRR FKKANTRALI KIFEYFSENL TAAGREKKLQ KKREELRRKR NSRSFGPRGS LDSIGSYRMS ADFG RPSLD YENLNQTMSQ ANRYNDGENL VDRTLQPNPE CRFAKDYWKN VKVGDIVRVH NNDEIPADMI LLSTSDVDGA CYVET KNLD GETNLKVRQS LKCSKIIKSS RDITRTKFWV ESEGPHANLY SYQGNFKWQD TQNGNIRNEP VNINNLLLRG CTLRNT KWA MGMVIFTGDD TKIMINAGVT PTKKSRISRE LNFSVILNFV LLFILCFTAG IVNGVYYKQK PRSRDYFEFG TIGGSAS TN GFVSFWVAVI LYQSLVPISL YISVEIIKTA QAIFIYTDVL LYNAKLDYPC TPKSWNISDD LGQIEYIFSD KTGTLTQN V MEFKKCTING VSYGRAYTEA LAGLRKRQGV DVESEGRREK EEIAKDRETM IDELRSMSDN TQFCPEDLTF VSKEIVEDL KGSSGDHQQK CCEHFLLALA LCHSVLVEPN KDDPKKLDIK AQSPDESALV STARQLGYSF VGSSKSGLIV EIQGVQKEFQ VLNVLEFNS SRKRMSCIIK IPGSTPKDEP KALLICKGAD SVIYSRLDRT QNDATLLEKT ALHLEEYATE GLRTLCLAQR E LTWSEYER WVKTYDVAAA SVTNREEELD KVTDVIEREL ILLGGTAIED RLQDGVPDSI ALLAEAGIKL WVLTGDKVET AI NIGFSCN VLNNDMELLV VKASGEDVEE FGSDPIQVVN NLVTKYLREK FGMSGSEEEL KEAKREHGLP QGNFAVIIDG DAL KVALNG EEMRRKFLLL CKNCKAVLCC RVSPAQKAAV VKLVKKTLDV MTLAIGDGSN DVAMIQSADV GVGIAGEEGR QAVM CSDYA IGQFRYVTRL VLVHGKWCYK RLAEMIPQFF YKNVIFTLSL FWYGIYNNFD GSYLFEYTYL TFYNLAFTSV PVILL AVLD QDVSDTVSML VPQLYRVGIL RKEWNQTKFL WYMLDGVYQS VICFFFPYLA YHKNMVVTEN GLGLDHRYFV GVFVTA IAV TSCNFYVFME QYRWDWFCGL FICLSLAVFY GWTGIWTSSS SSNEFYKGAA RVFAQPAYWA VLFVGVLFCL LPRFTID CI RKIFYPKDIE IVREMWLRGD FDLYPQGYDP TDPSRPRINE IRPLTDFKEP ISLDTHFDGV SHSQETIVTE EIPMSILN G EQGSRKGYRV STTLERRDQL SPVTTTNNLP RRSMASARGN KLRTSLDRTR EEMLANHQLD TRYSVERARA SLDLPGINH AETLLSQRSR DR |
-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: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 47.490395 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #6: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ![]() ChemComp-ALF: |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #9: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 9 / Number of copies: 1 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ![]() ChemComp-MAN: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266218 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |