[English] 日本語
Yorodumi
- EMDB-43979: Cryo-EM structure of GSSG-bound Ycf1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43979
TitleCryo-EM structure of GSSG-bound Ycf1
Map data
Sample
  • Organelle or cellular component: Yeast Cadmium Factor 1 bound with oxidized glutathione
    • Protein or peptide: Metal resistance protein YCF1
  • Ligand: OXIDIZED GLUTATHIONE DISULFIDE
KeywordsGSSG / MEMBRANE 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: 3.24 Å
AuthorsSoong TH / Hotze C / Raghav D / Khandelwal NK / Tomasiak TM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI156270 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of GSSG-bound Ycf1
Authors: Soong TH / Hotze C / Raghav D / Khandelwal NK / Tomasiak TM
History
DepositionMar 7, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43979.png

Downloads & links

-
Map

FileDownload / File: emd_43979.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 440 pix.
= 300.96 Å		0.68 Å/pix.
x 440 pix.
= 300.96 Å		0.68 Å/pix.
x 440 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.684 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.47132054 - 0.7640018
Average (Standard dev.)0.00038563905 (±0.015702568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_43979_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43979_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Yeast Cadmium Factor 1 bound with oxidized glutathione

EntireName: Yeast Cadmium Factor 1 bound with oxidized glutathione
Components
  • Organelle or cellular component: Yeast Cadmium Factor 1 bound with oxidized glutathione
    • Protein or peptide: Metal resistance protein YCF1
  • Ligand: OXIDIZED GLUTATHIONE DISULFIDE

-
Supramolecule #1: Yeast Cadmium Factor 1 bound with oxidized glutathione

SupramoleculeName: Yeast Cadmium Factor 1 bound with oxidized glutathione
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Organelle: Vacuole
Molecular weightTheoretical: 175.985 KDa

-
Macromolecule #1: Metal resistance protein YCF1

MacromoleculeName: Metal resistance protein YCF1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type Cd2+ transporter
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 171.545344 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 DAISLRRA(SEP)D A(TPO)LG(SEP)IDFGD DENIAKREHR EQGKVKWNIY LEYAKACNP KSVCVFILFI VISMFLSVMG NVWLKHWSEV NSRYGSNPNA ARYLAIYFAL GIGSALATLI QTIVLWVFCT IHASKYLHNL MTNSVLRAP MTFFETTPIG RILNRFSNDI YKVDALLGRT FSQFFVNAVK VTFTITVICA TTWQFIFIII PLSVFYIYYQ Q YYLRTSRE LRRLDSITRS PIYSHFQETL GGLATVRGYS QQKRFSHINQ CRIDNNMSAF YPSINANRWL AYRLELIGSI II LGAATLS VFRLKQGTLT AGMVGLSLSY ALQITQTLNW IVRMTVEVET NIVSVERIKE YADLKSEAPL IVEGHRPPKE WPS QGDIKF NNYSTRYRPE LDLVLKHINI HIKPNEKVGI VGRTGAGKSS LTLALFRMIE ASEGNIVIDN IAINEIGLYD LRHK LSIIP QDSQVFEGTV RENIDPINQY TDEAIWRALE LSHLKEHVLS MSNDGLDAQL TEGGGNLSVG QRQLLCLARA MLVPS KILV LDEATAAVDV ETDKVVQETI RTAFKDRTIL TIAHRLNTIM DSDRIIVLDN GKVAEFDSPG QLLSDNKSLF YSLCME AGL VNEN

UniProtKB: Metal resistance protein YCF1

-
Macromolecule #2: OXIDIZED GLUTATHIONE DISULFIDE

MacromoleculeName: OXIDIZED GLUTATHIONE DISULFIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GDS
Molecular weightTheoretical: 612.631 Da
Chemical component information

ChemComp-GDS:
OXIDIZED GLUTATHIONE DISULFIDE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
Sugar embeddingMaterial: Vitreous ice
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 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: Ab initio CRYOSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191581
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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