[English] 日本語
Yorodumi
- EMDB-23069: Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23069
TitleStructure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
Map dataCryo-EM 3D map of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
Sample
  • Complex: S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
    • Protein or peptide: Phospholipid-transporting ATPase DNF1
    • Protein or peptide: Alkylphosphocholine resistance protein LEM3
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


glycosylceramide flippase activity / mating projection tip membrane / phosphatidylcholine flippase activity / phosphatidylserine flippase activity / phosphatidylserine floppase activity / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylcholine floppase activity / phosphatidylethanolamine flippase activity / cell septum ...glycosylceramide flippase activity / mating projection tip membrane / phosphatidylcholine flippase activity / phosphatidylserine flippase activity / phosphatidylserine floppase activity / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylcholine floppase activity / phosphatidylethanolamine flippase activity / cell septum / cellular bud neck / P-type phospholipid transporter / phospholipid translocation / establishment or maintenance of cell polarity / cell periphery / intracellular protein transport / endocytosis / membrane => GO:0016020 / endosome membrane / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein 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
LEM3 isoform 1 / Phospholipid-transporting ATPase DNF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBai L / You Q / Jain BK / Duan HD / Kovach A / Graham TR / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA231466 to H.L. and GM107978 to T.R.G. United States
CitationJournal: Elife / Year: 2020
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
DepositionDec 7, 2020-
Header (metadata) releaseJan 6, 2021-
Map releaseJan 6, 2021-
UpdateJan 6, 2021-
Current statusJan 6, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ky6
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23069.png

Downloads & links

-
Map

FileDownload / File: emd_23069.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3D map of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
Voxel sizeX=Y=Z: 0.826 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.014
Minimum - Maximum-0.06674196 - 0.10976057
Average (Standard dev.)0.00024004401 (±0.0027564045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8260.8260.826
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z231.280231.280231.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0670.1100.000

-
Supplemental data

-
Sample components

-
Entire : S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in t...

EntireName: S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
Components
  • Complex: S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
    • Protein or peptide: Phospholipid-transporting ATPase DNF1
    • Protein or peptide: Alkylphosphocholine resistance protein LEM3
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in t...

SupramoleculeName: S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo E1 state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant strain: ATCC 204508 / S288c

-
Macromolecule #1: Phospholipid-transporting ATPase DNF1

MacromoleculeName: Phospholipid-transporting ATPase DNF1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 178.000172 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: 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

-
Macromolecule #2: Alkylphosphocholine resistance protein LEM3

MacromoleculeName: Alkylphosphocholine resistance protein LEM3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 47.490395 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: 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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 473761

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more