[English] 日本語
Yorodumi
- EMDB-40692: Cleaved Ycf1p Dimer in the IFwide-beta conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40692
TitleCleaved Ycf1p Dimer in the IFwide-beta conformation
Map dataCleaved Ycf1p Dimer in the IFwide-beta conformation
Sample
  • Complex: Cleaved Ycf1p IFwide-beta Dimer
    • Protein or peptide: Metal resistance protein YCF1
    • Protein or peptide: Unknown peptide
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
KeywordsABC transporter / Dimer / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Atorvastatin ADME / Paracetamol ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport ...ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Atorvastatin ADME / Paracetamol ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport / ABC-family proteins mediated transport / vacuole fusion, non-autophagic / ABC-type glutathione S-conjugate transporter activity / ABC-type glutathione-S-conjugate transporter / fungal-type vacuole / fungal-type vacuole membrane / response to metal ion / ATPase-coupled transmembrane transporter activity / response to cadmium ion / glutathione metabolic process / cell redox homeostasis / transmembrane transport / membrane raft / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / ABC transporter TMD0 domain / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / ABC transporter TMD0 domain / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Metal resistance protein YCF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBickers SC / Benlekbir S / Rubinstein JL / Kanelis V
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-05835 Canada
CitationJournal: Nat Commun / Year: 2024
Title: Structure of a dimeric full-length ABC transporter.
Authors: Sarah C Bickers / Samir Benlekbir / John L Rubinstein / Voula Kanelis /
Abstract: Activities of ATP binding cassette (ABC) proteins are regulated by multiple mechanisms, including protein interactions, phosphorylation, proteolytic processing, and/or oligomerization of the ABC ...Activities of ATP binding cassette (ABC) proteins are regulated by multiple mechanisms, including protein interactions, phosphorylation, proteolytic processing, and/or oligomerization of the ABC protein itself. Here we present the structure of yeast cadmium factor 1 (Ycf1p) in its mature form following cleavage by Pep4p protease. Ycf1p, a C subfamily ABC protein (ABCC), is homologue of human multidrug resistance protein 1. Remarkably, a portion of cleaved Ycf1p forms a well-ordered dimer, alongside monomeric particles also present in solution. While numerous other ABC proteins have been proposed to dimerize, no high-resolution structures have been reported. Both phosphorylation of the regulatory (R) region and ATPase activity are lower in the Ycf1p dimer compared to the monomer, indicating that dimerization affects Ycf1p function. The interface between Ycf1p protomers features protein-protein interactions and contains bound lipids, suggesting that lipids stabilize the dimer. The Ycf1p dimer structure may inform the dimerization interfaces of other ABCC dimers.
History
DepositionMay 4, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40692.png

Downloads & links

-
Map

FileDownload / File: emd_40692.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCleaved Ycf1p Dimer in the IFwide-beta conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 350 pix.
= 360.5 Å		1.03 Å/pix.
x 350 pix.
= 360.5 Å		1.03 Å/pix.
x 350 pix.
= 360.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.71
Minimum - Maximum-3.6611788 - 5.976819
Average (Standard dev.)0.00018059637 (±0.13235357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 360.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map 1

Fileemd_40692_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_40692_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cleaved Ycf1p IFwide-beta Dimer

EntireName: Cleaved Ycf1p IFwide-beta Dimer
Components
  • Complex: Cleaved Ycf1p IFwide-beta Dimer
    • Protein or peptide: Metal resistance protein YCF1
    • Protein or peptide: Unknown peptide
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

-
Supramolecule #1: Cleaved Ycf1p IFwide-beta Dimer

SupramoleculeName: Cleaved Ycf1p IFwide-beta Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Metal resistance protein YCF1

MacromoleculeName: Metal resistance protein YCF1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type Cd2+ transporter
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 174.024141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGNLVSWAC KLCRSPEGFG PISFYGDFTQ CFIDGVILNL SAIFMITFGI RDLVNLCKKK HSGIKYRRNW IIVSRMALVL LEIAFVSLA SLNISKEEAE NFTIVSQYAS TMLSLFVALA LHWIEYDRSV VANTVLLFYW LFETFGNFAK LINILIRHTY E GIWYSGQT ...String:
MAGNLVSWAC KLCRSPEGFG PISFYGDFTQ CFIDGVILNL SAIFMITFGI RDLVNLCKKK HSGIKYRRNW IIVSRMALVL LEIAFVSLA SLNISKEEAE NFTIVSQYAS TMLSLFVALA LHWIEYDRSV VANTVLLFYW LFETFGNFAK LINILIRHTY E GIWYSGQT GFILTLFQVI TCASILLLEA LPKKPLMPHQ HIHQTLTRRK PNPYDSANIF SRITFSWMSG LMKTGYEKYL VE ADLYKLP RNFSSEELSQ KLEKNWENEL KQKSNPSLSW AICRTFGSKM LLAAFFKAIH DVLAFTQPQL LRILIKFVTD YNS ERQDDH SSLQGFENNH PQKLPIVRGF LIAFAMFLVG FTQTSVLHQY FLNVFNTGMY IKSALTALIY QKSLVLSNEA SGLS STGDI VNLMSVDVQK LQDLTQWLNL IWSGPFQIII CLYSLYKLLG NSMWVGVIIL VIMMPLNSFL MRIQKKLQKS QMKYK DERT RVISEILNNI KSLKLYAWEK PYREKLEEVR NNKELKNLTK LGCYMAVTSF QFNIVPFLVS CCTFAVFVYT EDRALT TDL VFPALTLFNL LSFPLMIIPM VLNSFIEASV SIGRLFTFFT NEELQPDSVQ RLPKVKNIGD VAINIGDDAT FLWQRKP EY KVALKNINFQ AKKGNLTCIV GKVGSGKTAL LSCMLGDLFR VKGFATVHGS VAYVSQVPWI MNGTVKENIL FGHRYDAE F YEKTIKACAL TIDLAILMDG DKTLVGEKGI SLSGGQKARL SLARAVYARA DTYLLDDPLA AVDEHVARHL IEHVLGPNG LLHTKTKVLA TNKVSALSIA DSIALLDNGE ITQQGTYDEI TKDADSPLWK LLNNYGKKNN GKSNEFGDSS ESSVRESSIP VEGELEQLQ KLNDLDFGNS DAISLRRASD ATLGSIDFGD DENIAKREHR EQGKVKWNIY LEYAKACNPK SVCVFILFIV I SMFLSVMG NVWLKHWSEV NSRYGSNPNA ARYLAIYFAL GIGSALATLI QTIVLWVFCT IHASKYLHNL MTNSVLRAPM TF FETTPIG RILNRFSNDI YKVDALLGRT FSQFFVNAVK VTFTITVICA TTWQFIFIII PLSVFYIYYQ QYYLRTSREL RRL DSITRS PIYSHFQETL GGLATVRGYS QQKRFSHINQ CRIDNNMSAF YPSINANRWL AYRLELIGSI IILGAATLSV FRLK QGTLT AGMVGLSLSY ALQITQTLNW IVRMTVEVET NIVSVERIKE YADLKSEAPL IVEGHRPPKE WPSQGDIKFN NYSTR YRPE LDLVLKHINI HIKPNEKVGI VGRTGAGKSS LTLALFRMIE ASEGNIVIDN IAINEIGLYD LRHKLSIIPQ DSQVFE GTV RENIDPINQY TDEAIWRALE LSHLKEHVLS MSNDGLDAQL TEGGGNLSVG QRQLLCLARA MLVPSKILVL DEATAAV DV ETDKVVQETI RTAFKDRTIL TIAHRLNTIM DSDRIIVLDN GKVAEFDSPG QLLSDNKSLF YSLCMEAGLV NENDYKDH D GDYKDHDIDY KDDDDK

UniProtKB: Metal resistance protein YCF1

-
Macromolecule #2: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.124378 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

-
Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Macromolecule #4: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadec...

MacromoleculeName: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate
type: ligand / ID: 4 / Number of copies: 2 / Formula: GP7
Molecular weightTheoretical: 673.901 Da
Chemical component information

ChemComp-GP7:
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate

-
Macromolecule #5: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 5 / Number of copies: 2 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Cleaved Ycf1p monomer in the IFwide-beta conformation
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71014
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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