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- EMDB-40451: E1435Q Ycf1 mutant in dephosphorylated state -

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Basic information

Entry
Database: EMDB / ID: EMD-40451
TitleE1435Q Ycf1 mutant in dephosphorylated state
Map dataSharpened cryosparc map used for model building and refinement.
Sample
  • Complex: Ycf1
    • Protein or peptide: Metal resistance protein YCF1
KeywordsABC transporter / 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 / vacuole fusion, non-autophagic / ABC-family proteins mediated transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / 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 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. ...: / 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 S288C (yeast) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsKhandelwal NK / Tomasiak TM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R00 GM11424 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01 AI156270 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for autoinhibition by the dephosphorylated regulatory domain of Ycf1.
Authors: Nitesh Kumar Khandelwal / Thomas M Tomasiak /
Abstract: Yeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding ...Yeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding Cassette (ABC) transporters characterized by long flexible linkers, notably the regulatory domain (R-domain). R-domain phosphorylation is necessary for activity, whereas dephosphorylation induces autoinhibition through an undefined mechanism. Because of its transient and dynamic nature, no structure of the dephosphorylated Ycf1 exists, limiting understanding of this R-domain regulation. Here, we capture the dephosphorylated Ycf1 using cryo-EM and show that the unphosphorylated R-domain indeed forms an ordered structure with an unexpected hairpin topology bound within the Ycf1 substrate cavity. This architecture and binding mode resemble that of a viral peptide inhibitor of an ABC transporter and the secreted bacterial WXG peptide toxins. We further reveal the subset of phosphorylation sites within the hairpin turn that drive the reorganization of the R-domain conformation, suggesting a mechanism for Ycf1 activation by phosphorylation-dependent release of R-domain mediated autoinhibition.
History
DepositionApr 11, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40451.png

Downloads & links

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Map

FileDownload / File: emd_40451.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryosparc map used for model building and refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.984 Å		1.07 Å/pix.
x 360 pix.
= 384.984 Å		1.07 Å/pix.
x 360 pix.
= 384.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0694 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.467
Minimum - Maximum-2.0100977 - 3.338302
Average (Standard dev.)-0.00045418934 (±0.066694155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.98398 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened cryosparc map.

Fileemd_40451_additional_1.map
AnnotationUnsharpened cryosparc map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from cryosparc reconstruction used in...

Fileemd_40451_half_map_1.map
AnnotationHalf map 1 from cryosparc reconstruction used in final model building and refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from cryosparc reconstruction used in...

Fileemd_40451_half_map_2.map
AnnotationHalf map 2 from cryosparc reconstruction used in final model building and refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ycf1

EntireName: Ycf1
Components
  • Complex: Ycf1
    • Protein or peptide: Metal resistance protein YCF1

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Supramolecule #1: Ycf1

SupramoleculeName: Ycf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 176.66831 KDa

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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) / Strain: Saccharomyces cerevisiae
Molecular weightTheoretical: 176.209594 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASDYKDDDD KGALEVLFQG PSSPMAGNLV SWACKLCRSP EGFGPISFYG DFTQCFIDGV ILNLSAIFMI TFGIRDLVNL CKKKHSGIK YRRNWIIVSR MALVLLEIAF VSLASLNISK EEAENFTIVS QYASTMLSLF VALALHWIEY DRSVVANTVL L FYWLFETF ...String:
MASDYKDDDD KGALEVLFQG PSSPMAGNLV SWACKLCRSP EGFGPISFYG DFTQCFIDGV ILNLSAIFMI TFGIRDLVNL CKKKHSGIK YRRNWIIVSR MALVLLEIAF VSLASLNISK EEAENFTIVS QYASTMLSLF VALALHWIEY DRSVVANTVL L FYWLFETF GNFAKLINIL IRHTYEGIWY SGQTGFILTL FQVITCASIL LLEALPKKPL MPHQHIHQTL TRRKPNPYDS AN IFSRITF SWMSGLMKTG YEKYLVEADL YKLPRNFSSE ELSQKLEKNW ENELKQKSNP SLSWAICRTF GSKMLLAAFF KAI HDVLAF TQPQLLRILI KFVTDYNSER QDDHSSLQGF ENNHPQKLPI VRGFLIAFAM FLVGFTQTSV LHQYFLNVFN TGMY IKSAL TALIYQKSLV LSNEASGLSS TGDIVNLMSV DVQKLQDLTQ WLNLIWSGPF QIIICLYSLY KLLGNSMWVG VIILV IMMP LNSFLMRIQK KLQKSQMKYK DERTRVISEI LNNIKSLKLY AWEKPYREKL EEVRNNKELK NLTKLGCYMA VTSFQF NIV PFLVSCCTFA VFVYTEDRAL TTDLVFPALT LFNLLSFPLM IIPMVLNSFI EASVSIGRLF TFFTNEELQP DSVQRLP KV KNIGDVAINI GDDATFLWQR KPEYKVALKN INFQAKKGNL TCIVGKVGSG KTALLSCMLG DLFRVKGFAT VHGSVAYV S QVPWIMNGTV KENILFGHRY DAEFYEKTIK ACALTIDLAI LMDGDKTLVG EKGISLSGGQ KARLSLARAV YARADTYLL DDPLAAVDEH VARHLIEHVL GPNGLLHTKT KVLATNKVSA LSIADSIALL DNGEITQQGT YDEITKDADS PLWKLLNNYG KKNNGKSNE FGDSSESSVR ESSIPVEGEL EQLQKLNDLD FGNSDAISLR RASDATLGSI DFGDDENIAK REHREQGKVK W NIYLEYAK ACNPKSVCVF ILFIVISMFL SVMGNVWLKH WSEVNSRYGS NPNAARYLAI YFALGIGSAL ATLIQTIVLW VF CTIHASK YLHNLMTNSV LRAPMTFFET TPIGRILNRF SNDIYKVDAL LGRTFSQFFV NAVKVTFTIT VICATTWQFI FII IPLSVF YIYYQQYYLR TSRELRRLDS ITRSPIYSHF QETLGGLATV RGYSQQKRFS HINQCRIDNN MSAFYPSINA NRWL AYRLE LIGSIIILGA ATLSVFRLKQ GTLTAGMVGL SLSYALQITQ TLNWIVRMTV EVETNIVSVE RIKEYADLKS EAPLI VEGH RPPKEWPSQG DIKFNNYSTR YRPELDLVLK HINIHIKPNE KVGIVGRTGA GKSSLTLALF RMIEASEGNI VIDNIA INE IGLYDLRHKL SIIPQDSQVF EGTVRENIDP INQYTDEAIW RALELSHLKE HVLSMSNDGL DAQLTEGGGN LSVGQRQ LL CLARAMLVPS KILVLDQATA AVDVETDKVV QETIRTAFKD RTILTIAHRL NTIMDSDRII VLDNGKVAEF DSPGQLLS D NKSLFYSLCM EAGLVNENGL VPRGSSAHHH HHHHHHHGA

UniProtKB: Metal resistance protein YCF1

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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

Concentration10.56 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
50.0 mMTristris(hydroxymethyl)aminomethane

Details: Solution were made fresh in cold distilled water and final pH was adjusted to 7.0 with HCl of cold buffer. The digitonin detergent was added to final .06 % in buffer after pH adjustment.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5904 / Average exposure time: 3.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5424196 / Details: Relion autopick
Startup modelType of model: OTHER / Details: Ab-initio Model generated in Relion.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 73611
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9-f1


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-8sg4:
E1435Q Ycf1 mutant in dephosphorylated state

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