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

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ID or keywords:

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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 / Cytoprotection by HMOX1 / Aspirin ADME / Paracetamol ADME / Atorvastatin ADME / Transport of RCbl within the body / Synthesis of Leukotrienes (LT) and Eoxins (EX) ...ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Cytoprotection by HMOX1 / Aspirin ADME / Paracetamol ADME / Atorvastatin ADME / Transport of RCbl within the body / Synthesis of Leukotrienes (LT) and Eoxins (EX) / 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 / 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 / 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. / ATPases associated with a variety of cellular activities ...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: To Be Published
Title: E1435Q Ycf1 mutant in dephosphorylated state
Authors: Khandelwal NK / Tomasiak TM
History
DepositionApr 11, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 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.
Voxel sizeX=Y=Z: 1.0694 Å
Density
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 chloridesodium 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
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
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
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.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
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
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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