5JQM | pdb_00005jqm

Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 1.5 Angstroms Resolution

• PDB DOI: https://doi.org/10.2210/pdb5JQM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-05-05 Released: 2017-07-12 
• Deposition Author(s): Lu, J., Chan, K.C., Zhai, Y., Fan, J., Sun, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Molecular mechanism of mitochondrial phosphatidate transfer by Ups1

Lu, J., Chan, C., Yu, L., Fan, J., Sun, F., Zhai, Y.

(2020) Commun Biol 

• DOI: https://doi.org/10.1038/s42003-020-01121-x

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 97.04 kDa 
• Atom Count: 6,421 
• Modeled Residue Count: 706 
• Deposited Residue Count: 849 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein UPS1, mitochondrial,Mitochondrial distribution and morphology protein 35	A, B, C	283	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UPS1, YLR193C, MDM35, YKL053C-A Membrane Entity: Yes
UniProt
Find proteins for O60200 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O60200  Go to UniProtKB:  O60200
Find proteins for Q05776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05776  Go to UniProtKB:  Q05776
UniProt Groups	O60200Q05776

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.563	α = 90
b = 68.29	β = 102.1
c = 105.137	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data processing
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Lu, J., Chan, K.C., Zhai, Y., Fan, J., Sun, F.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2020-09-02
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary