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- EMDB-59064: Cryo-EM structure of Saccharomyces cerevisiae Erv14-Qdr2 complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-59064
TitleCryo-EM structure of Saccharomyces cerevisiae Erv14-Qdr2 complex in detergent
Map data
Sample
  • Organelle or cellular component: Saccharomyces cerevisiae Qdr2-Erv14 complex in detergent
    • Protein or peptide: ER-derived vesicles protein ERV14
    • Protein or peptide: Quinidine resistance protein 2
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ERGOSTEROL
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate
KeywordsCargo Receptor / Cornichon / Major Facilitator Superfamily / Drug:Proton Antiporter / Membrane Protein / Erv14 / Qdr2 / Lipid-Mediated Interface
Function / homology
Function and homology information


axial cellular bud site selection / threonine efflux transmembrane transporter activity / amino acid export across plasma membrane / negative regulation of receptor localization to synapse / ascospore formation / copper ion export / regulation of AMPA receptor activity / COPII-coated ER to Golgi transport vesicle / monoatomic cation transmembrane transporter activity / cargo receptor activity ...axial cellular bud site selection / threonine efflux transmembrane transporter activity / amino acid export across plasma membrane / negative regulation of receptor localization to synapse / ascospore formation / copper ion export / regulation of AMPA receptor activity / COPII-coated ER to Golgi transport vesicle / monoatomic cation transmembrane transporter activity / cargo receptor activity / potassium ion import across plasma membrane / xenobiotic transmembrane transporter activity / endoplasmic reticulum to Golgi vesicle-mediated transport / transmembrane transporter activity / cell periphery / transmembrane transport / signaling receptor binding / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Quinidine resistance protein 2 / ER-derived vesicles protein ERV14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsTunyi J / Adams O / Newstead S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust219531/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Cornichon receptors couple membrane adaptation to cargo selection during ER export
Authors: Tunyi J / Adams O / Forrest L / Parker JL / Newstead S
History
DepositionJul 20, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59064.png

Downloads & links

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Map

FileDownload / File: emd_59064.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.937655 - 6.186824
Average (Standard dev.)0.0015574374 (±0.12599337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened Map

Fileemd_59064_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_59064_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_59064_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae Qdr2-Erv14 complex in detergent

EntireName: Saccharomyces cerevisiae Qdr2-Erv14 complex in detergent
Components
  • Organelle or cellular component: Saccharomyces cerevisiae Qdr2-Erv14 complex in detergent
    • Protein or peptide: ER-derived vesicles protein ERV14
    • Protein or peptide: Quinidine resistance protein 2
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ERGOSTEROL
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate

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Supramolecule #1: Saccharomyces cerevisiae Qdr2-Erv14 complex in detergent

SupramoleculeName: Saccharomyces cerevisiae Qdr2-Erv14 complex in detergent
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: ER-derived vesicles protein ERV14

MacromoleculeName: ER-derived vesicles protein ERV14 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.940873 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MGAWLFILAV VVNCINLFGQ VHFTILYADL EADYINPIEL CSKVNKLITP EAALHGALSL LFLLNGYWFV FLLNLPVLAY NLNKIYNKV QLLDATEIFR TLGKHKRESF LKLGFHLLMF FFYLYRMIMA LIAESGDDFD YKDDDDK

UniProtKB: ER-derived vesicles protein ERV14

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Macromolecule #2: Quinidine resistance protein 2

MacromoleculeName: Quinidine resistance protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 60.527609 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAGATSSIIR ENDFEDELAE SMQSYNRETA DKLALTRTES VKPEPEITAP PHSRFSRSFK TVLIAQCAFT GFFSTIAGAI YYPVLSVIE RKFDIDEELV NVTVVVYFVF QGLAPTFMGG FADSLGRRPV VLVAIVIYFG ACIGLACAQT YAQIIVLRCL Q AAGISPVI ...String:
MAGATSSIIR ENDFEDELAE SMQSYNRETA DKLALTRTES VKPEPEITAP PHSRFSRSFK TVLIAQCAFT GFFSTIAGAI YYPVLSVIE RKFDIDEELV NVTVVVYFVF QGLAPTFMGG FADSLGRRPV VLVAIVIYFG ACIGLACAQT YAQIIVLRCL Q AAGISPVI AINSGIMGDV TTRAERGGYV GYVAGFQVLG SAFGALIGAG LSSRWGWRAI FWFLAIGSGI CFLASFLILP ET KRNISGN GSVTPKSYLN RAPILVLPTV RKSLHLDNPD YETLELPTQL NLLAPFKILK AYEICILMLV AGLQFAMYTT HLT ALSTAL SKQYHLTVAK VGLCYLPSGI CTLCSIVIAG RYLNWNYRRR LKYYQNWLGK KRSKLLEEHD NDLNLVQRII ENDP KYTFN IFKARLQPAF VTLLLSSSGF CAYGWCITVK APLAAVLCMS GFASLFSNCI LTFSTTLIVD LFPTKTSTAT GCLNL FRCI LSAVFIAALS KMVEKMKFGG VFTFLGALTS SSSILLFILL RKGKELAFKR KKQELGVNGE NLYFQ

UniProtKB: Quinidine resistance protein 2

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 4 / Number of copies: 3 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL

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Macromolecule #5: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate

MacromoleculeName: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate / type: ligand / ID: 5 / Number of copies: 1 / Formula: NKN
Molecular weightTheoretical: 382.429 Da
Chemical component information

ChemComp-NKN:
(2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate

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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

Concentration4 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, 150 mM NaCl, 0.0015% (w/v)LMNG:CHS
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsData Collected at 2, 4 & 6.1 mg/mL

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Number real images: 58208 / Average exposure time: 2.4 sec. / Average electron dose: 39.1 e/Å2
Details: First Collection = 3 Grids, 26205 Images, Total Dose 39.1, 2.4 s Per Exposure Second Collection = 1 Grid, 32003 Images, Total Dose 41.1, 2.39 s Per Exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 21293856
CTF correctionSoftware - Name: SIMPLE (ver. 3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 373696
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

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

PDB-32pz:
Cryo-EM structure of Saccharomyces cerevisiae Erv14-Qdr2 complex in detergent

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