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- EMDB-0872: Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P... -

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Basic information

Entry
Database: EMDB / ID: EMD-0872
TitleCryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state
Map data
Sample
  • Complex: Heterodimer of Dnf1-Cdc50
    • Protein or peptide: Phospholipid-transporting ATPase
    • Protein or peptide: Cdc50
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsP-type ATPase / lipid flippase / LIPID TRANSPORT
Function / homology
Function and homology information


phosphatidylserine floppase activity / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / P-type phospholipid transporter / endosome membrane / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site ...CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Phospholipid-transporting ATPase DNF1 / Phospholipid-transporting ATPase accessory subunit CDC50
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsHe Y / Xu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870835 China
CitationJournal: Protein Cell / Year: 2020
Title: Structures of a P4-ATPase lipid flippase in lipid bilayers.
Authors: Yilin He / Jinkun Xu / Xiaofei Wu / Long Li /
History
DepositionNov 19, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lcp
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0872.png

Downloads & links

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Map

FileDownload / File: emd_0872.map.gz / Format: CCP4 / Size: 87.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 284 pix.
= 299.62 Å		1.06 Å/pix.
x 284 pix.
= 299.62 Å		1.06 Å/pix.
x 284 pix.
= 299.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08409796 - 0.14477704
Average (Standard dev.)0.00016820052 (±0.0027133294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions284284284
Spacing284284284
CellA=B=C: 299.62 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z284284284
origin x/y/z0.0000.0000.000
length x/y/z299.620299.620299.620
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS284284284
D min/max/mean-0.0840.1450.000

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Supplemental data

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Sample components

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Entire : Heterodimer of Dnf1-Cdc50

EntireName: Heterodimer of Dnf1-Cdc50
Components
  • Complex: Heterodimer of Dnf1-Cdc50
    • Protein or peptide: Phospholipid-transporting ATPase
    • Protein or peptide: Cdc50
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Heterodimer of Dnf1-Cdc50

SupramoleculeName: Heterodimer of Dnf1-Cdc50 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Macromolecule #1: Phospholipid-transporting ATPase

MacromoleculeName: Phospholipid-transporting ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 175.379531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

UniProtKB: Phospholipid-transporting ATPase DNF1

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Macromolecule #2: Cdc50

MacromoleculeName: Cdc50 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 46.452312 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

UniProtKB: Phospholipid-transporting ATPase accessory subunit CDC50

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #9: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 9 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #10: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 10 / Number of copies: 1 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2820251
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 249694
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 8 / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6lcp:
Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state

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