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- EMDB-43985: Tetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide co... -

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Basic information

Entry
Database: EMDB / ID: EMD-43985
TitleTetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
Map data
Sample
  • Organelle or cellular component: Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
    • Protein or peptide: Metal resistance protein YCF1
KeywordsABC-transporter / ycf1 / r-domain / phosphorylation / heavy metal / 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 / Paracetamol ADME / Atorvastatin 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 / Paracetamol ADME / Atorvastatin 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 / ABC-type glutathione S-conjugate transporter activity / response to metal ion / fungal-type vacuole membrane / 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 (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsCarvalho RSA / Rasel MSI / Khandelwal NK / Tomasiak TM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01 AI156270 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH S10 OD011981 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation
Authors: Carvalho RSA / Rasel MSI / Khandelwal NK / Tomasiak TM
History
DepositionMar 7, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43985.png

Downloads & links

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Map

FileDownload / File: emd_43985.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.)
0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.24820127 - 0.5574108
Average (Standard dev.)0.000040163784 (±0.012052121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 361.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43985_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43985_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation

EntireName: Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
Components
  • Organelle or cellular component: Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
    • Protein or peptide: Metal resistance protein YCF1

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Supramolecule #1: Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation

SupramoleculeName: Phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: c-AMP PKA treated E1435Q Ycf1 mutant
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 176462 kDa/nm

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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)
Molecular weightTheoretical: 176.263234 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 FGNSDAI(SEP)LR RA(SEP)DA(TPO)LG(SEP)I DFGDD ENIA KREHREQGKV KWNIYLEYAK ACNPKSVCVF ILFIVISMFL SVMGNVWLKH WSEVNSRYGS NPNAARYLAI YFALGI GSA LATLIQTIVL WVFCTIHASK YLHNLMTNSV LRAPMTFFET TPIGRILNRF SNDIYKVDAL LGRTFSQFFV NAVKVTF TI TVICATTWQF IFIIIPLSVF YIYYQQYYLR TSRELRRLDS ITRSPIYSHF QETLGGLATV RGYSQQKRFS HINQCRID N NMSAFYPSIN ANRWLAYRLE LIGSIIILGA ATLSVFRLKQ GTLTAGMVGL SLSYALQITQ TLNWIVRMTV EVETNIVSV ERIKEYADLK SEAPLIVEGH RPPKEWPSQG DIKFNNYSTR YRPELDLVLK HINIHIKPNE KVGIVGRTGA GKSSLTLALF RMIEASEGN IVIDNIAINE IGLYDLRHKL SIIPQDSQVF EGTVRENIDP INQYTDEAIW RALELSHLKE HVLSMSNDGL D AQLTEGGG NLSVGQRQLL CLARAMLVPS KILVLDQATA AVDVETDKVV QETIRTAFKD RTILTIAHRL NTIMDSDRII VL DNGKVAE FDSPGQLLSD NKSLFYSLCM EAGLVNENGL VPRGSSAHHH HHHHHH

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

Concentration5.94 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMTRIS-HclTris
300.0 mMNaClNaCl
0.02 %GDNGDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283 K / Instrument: LEICA EM GP
Details: 5 microliters of sample of concentrated E1435Q (5.94 mg/mL) PKA-treated Ycf1 sample was applied to QF-1.2/1,3 Au grid. Grids were place inside of a Leica EM GP2 equilibrated at 10 degress ...Details: 5 microliters of sample of concentrated E1435Q (5.94 mg/mL) PKA-treated Ycf1 sample was applied to QF-1.2/1,3 Au grid. Grids were place inside of a Leica EM GP2 equilibrated at 10 degress Celcius amd 80% humidity. Following 10 seconds incubation, the side of the grid to which the sample was applied was blotted on a Whatman 1 paper (3.5 seconds) then immediately plunge frrozen in liquid ethan equilibrated at -185 degree Celcius..
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 8587 / Average exposure time: 0.9 sec. / Average electron dose: 54.0 e/Å2
Details: Movies were collected at 22,500X magnification with automated super-resolution mode and defocus range of -0.9 to -2.1 micrometer. Moview frames cotained 60 frames with a per frame expousre ...Details: Movies were collected at 22,500X magnification with automated super-resolution mode and defocus range of -0.9 to -2.1 micrometer. Moview frames cotained 60 frames with a per frame expousre of 0.9 electrons per angstrom squared (54 electron/angstrom square total dose)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4840688
Details: Manual and auto particle picking and extraction from 8380 curated micropgrahs
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 68169
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

9109


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9ayc:
Tetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation

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