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- EMDB-0873: Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0873 | |||||||||
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Title | Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP state | |||||||||
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Function / homology | ![]() ATPase-coupled intramembrane lipid transporter activity / phospholipid transport / P-type phospholipid transporter / phospholipid translocation / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | He Y / Xu J / Wu X / Li L | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of a P4-ATPase lipid flippase in lipid bilayers. Authors: Yilin He / Jinkun Xu / Xiaofei Wu / Long Li / ![]() | |||||||||
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 | ![]() | 6.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
Images | ![]() | 50.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lcrMC ![]() 0872C ![]() 6lcpC M: atomic model generated by this map C: citing same article ( |
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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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Voxel size | X=Y=Z: 1.055 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 : Heterodimer of Dnf1-Cdc50
Entire | Name: Heterodimer of Dnf1-Cdc50 |
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Components |
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-Supramolecule #1: Heterodimer of Dnf1-Cdc50
Supramolecule | Name: Heterodimer of Dnf1-Cdc50 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Phospholipid-transporting ATPase
Macromolecule | Name: Phospholipid-transporting ATPase / 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: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 175.379531 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAPPQEEGGG NGTELSMQRS RWATRRLTVK SGARKRLSLM TRAQAKNSAT EKRQSGVTDD GSPAADGDQK EGSISSSNNG GSAPRKLYF NLPLPPELKD EEGHPIQQFP RNKIRTAKYT PLSFIPKNLW FQFHNIANIF FLFLVILVIF PIFGGVNPGL N SVPLIVII ...String: MAPPQEEGGG NGTELSMQRS RWATRRLTVK SGARKRLSLM TRAQAKNSAT EKRQSGVTDD GSPAADGDQK EGSISSSNNG GSAPRKLYF NLPLPPELKD EEGHPIQQFP RNKIRTAKYT PLSFIPKNLW FQFHNIANIF FLFLVILVIF PIFGGVNPGL N SVPLIVII TVTAIKDAIE DYRRTILDIE LNNAPVHRLQ GWENVNVEKD NVSLWRRFKK ANSRFFGSIW HLIERLWKED AQ SMRQRFA SADPRMSIET RTAPWDPSHR RSVASHTEEI QMTPVPSPVP HDPDVPTVSS AIENEATLLQ NLKGDLINHE IPV SGKARF HKDAWKNLVV GDFVRIYNDD ELPADIIILA TSDPDGACYV ETKNLDGETN LKVRQALRCG RTLKHARDCE RAQF VIESE PPQPNLYKYN GAIRWKQRVP WDPHGEPREM SEPIGIDNLL LRGCHLRNTE WALGVVVFTG HDTKIMMNAG ITPSK RARI ARELNFNVIC NFGILLIMCL IAAIANGIAW GKTDASLAWF EYGSIGGTPA LTGFITFWAA VIVFQNLVPI SLYISL EIV RTLQAFFIYS DVGMYYEKID QPCIPKSWNI SDDVGQIEYI FSDKTGTLTQ NVMEFKKATI NGQPYGEAYT EAQAGMD RR RGINVEEEAK VIREEIAAAK VRAIRGLREL HDNPYLHDED MTFIAPDFVE DLAGKNGPEQ QQATEHFMLA LALCHTVV A EKQPGDPPKM IFKAQSPDEA ALVATARDMG FTVLGMSDGG INVNVMGKDM HFPVLSIIEF NSSRKRMSTI VRMPDGRIL LFCKGADSVI YSRLKKGEQA DMRRETAQHL EMFAVEGLRT LCIAERELSE EEYREWRREH DLAATALENR EEKLEEVADK IERDLTLLG GTAIEDRLQD GVPDTIALLA DAGIKLWVLT GDKVETAINI GFSCNLLNND MDLLRLQVNE SDASTEDDYL Q LAEEQLKT NLERFNMTGD DEELKRARKD HNAPSPTYAL VIDGFTLRWV LSDSLKQKFL LLCKQCKSVL CCRVSPAQKA AV VSMVKNG LDVMTLSIGD GANDVAMIQE ADVGVGIAGE EGRQAVMSSD FAIGQFRFLQ RLVLVHGRWS YRRLAETISN FFY KNMIWT WSIFWYQCYC NFDIAYIFEY TYILMFNLFF TSVPVILMGV LDQDVSDTVS LAVPQLYRRG IERKEWTQTK FWLY MIDGV YQSVMSFFIP FIFVVLTPTA AGNGLDVSER TRLGAYIAHP AVITINGYIL INTYRWDWLM LLSIVLSDVF IFFWT GVYT ATTYSAGFYQ AAPQVYQELT FWMCLIVTPA LCLLPRLVVK CIQKQRFPYD VDIIREQANR GDFAAADAAA VAALGG PER VEGESLGSLS SSGKGSGRSK KSKHQQYASV DEDRRPIYPP SIATHNTRAQ NGSDGTTYIM QSRTSTELQQ EMPFDRD RE EETPAVRPSI ERTRPSYDRI RRSIDRVRPS FEASNDFTSA ARLSRIESTH SSLGHTYSHQ RESYAGESSG AQQGQEPG Q RRFNLATVRK RGLSAFSKKS IDTTEGEPPR EPPM |
-Macromolecule #2: Cdc50
Macromolecule | Name: Cdc50 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 46.452312 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAPRRRRGAG QDGSDDGRSD SDAPKNRPPN TAFRQQRMRA WQCVLTPKLI VTVFSILAAI YLGFGAWLTY LAHTVRDLKI DYTDCLTSA PKDDFETIPQ NHITAHFSAK DSTFDPYKAQ WKTTEREVQV ANYTDNRQFC IVRFNIPEDL QPTISFFYYL E NFYQNHRR ...String: MAPRRRRGAG QDGSDDGRSD SDAPKNRPPN TAFRQQRMRA WQCVLTPKLI VTVFSILAAI YLGFGAWLTY LAHTVRDLKI DYTDCLTSA PKDDFETIPQ NHITAHFSAK DSTFDPYKAQ WKTTEREVQV ANYTDNRQFC IVRFNIPEDL QPTISFFYYL E NFYQNHRR YVNSFNAKQL LGDAVDGKTI NDSTCDPITH DPKGTGKIVY PCGLVANSIF NDTFSSPLAL AVRNSSDSSR PY NMTTKGI AWPGLKDLYG KTSYSLDQIV PPPNWERRYK YGYQENNPPP DLKTDELFQN WMMLAAAPNF YKLYQKNDTH PML AGQYEI EIESNFDVTV YKGRKAFVIT TLSTMGSRNI WPGIIFLIVG GICLVLDIYF ILSFFIWRPR KLGDPSYLSW NQPS APGGH SS |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: ACP |
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Molecular weight | Theoretical: 505.208 Da |
Chemical component information | ![]() ChemComp-ACP: |
-Macromolecule #7: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...
Macromolecule | Name: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine type: ligand / ID: 7 / Number of copies: 1 / Formula: P5S |
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Molecular weight | Theoretical: 792.075 Da |
Chemical component information | ![]() ChemComp-P5S: |
-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: |
-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: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6lcr: |