9AYC

Tetra-phosphorylated, E1435Q Ycf1 mutant in inward-facing wide conformation

• PDB DOI: https://doi.org/10.2210/pdb9AYC/pdb
• EM Map EMD-43985: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-03-07 Released: 2024-08-21 
• Deposition Author(s): Carvalho, R.S.A., Rasel, M.S.I., Khandelwal, N.K., Tomasiak, T.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation

Carvalho, R.S.A., Rasel, M.S.I., Khandelwal, N.K., Tomasiak, T.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 176.26 kDa 
• Atom Count: 11,776 
• Modelled Residue Count: 1,481 
• Deposited Residue Count: 1,557 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal resistance protein YCF1	A	1,557	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: YCF1, YDR135C, YD9302.11C EC: 7.2.2.2 (PDB Primary Data), 7.6.2.3 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P39109 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39109  Go to UniProtKB:  P39109

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
RECONSTRUCTION	cryoSPARC	4.2.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Carvalho, R.S.A., Rasel, M.S.I., Khandelwal, N.K., Tomasiak, T.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH R01 AI156270
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH S10 OD011981

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release