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- PDB-32qb: Cryo-EM structure of Saccharomyces cerevisiae Erv14-Qdr2 complex ... -

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Basic information

Entry
Database: PDB / ID: 32qb
TitleCryo-EM structure of Saccharomyces cerevisiae Erv14-Qdr2 complex in lipid nanodiscs (single Erv14 assembly)
Components
  • ER-derived vesicles protein ERV14
  • Quinidine resistance protein 2
KeywordsMEMBRANE PROTEIN / Cargo Receptor / Cornichon / Major Facilitator Superfamily / Drug:Proton Antiporter / 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
ERGOSTEROL / Chem-NKN / CHOLESTEROL HEMISUCCINATE / Quinidine resistance protein 2 / ER-derived vesicles protein ERV14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsAdams, O. / Parker, J.L. / Newstead, S.
Funding support United Kingdom, 1items
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, J.L. / Newstead, S.
History
DepositionJul 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ER-derived vesicles protein ERV14
B: Quinidine resistance protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,05112
Polymers77,4682
Non-polymers4,58310
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ER-derived vesicles protein ERV14


Mass: 16940.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERV14, YGL054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: P53173
#2: Protein Quinidine resistance protein 2


Mass: 60527.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: QDR2, YIL121W / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: P40474
#3: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H44O
#5: Chemical ChemComp-NKN / (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate / 14:0 LPA / myristoyl lysophosphatidic acid


Mass: 382.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H35O7P
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Saccharomyces cerevisiae Qdr2-Erv14 complex in lipid nanodiscs (single Erv14 assembly)
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5460
Buffer solutionpH: 7.5 / Details: 20 mM HEPES, 150 mM NaCl
SpecimenConc.: 3.97 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 49836
Details: First Collection = 15426 Images, Total Dose 40, 1.8 s Per Exposure Second Collection = 34410 Images, Total Dose 39.9, 1.8 s Per Exposure

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Processing

EM software
IDNameVersionCategory
1SIMPLE3particle selection
2EPUimage acquisition
4SIMPLE3CTF correction
9PHENIX1.29.1-4487model refinement
10Coot0.9.8.2model refinement
11ISOLDE1.10.1model refinement
12cryoSPARC4.7.1initial Euler assignment
13cryoSPARC4.7.1final Euler assignment
15cryoSPARC4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30817460
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168498 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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