5JQL

Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 2.9 Angstroms Resolution

• PDB DOI: https://doi.org/10.2210/pdb5JQL/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• 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: 2.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

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: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

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

Macromolecule Content

• Total Structure Weight: 190.19 kDa 
• Atom Count: 11,018 
• Modelled Residue Count: 1,432 
• Deposited Residue Count: 1,650 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein UPS1, mitochondrial	A, E, I, K	189	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UPS1, YLR193C
UniProt
Find proteins for Q05776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05776  Go to UniProtKB:  Q05776

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial distribution and morphology protein 35	B, D, F, J, L	86	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MDM35, YKL053C-A
UniProt
Find proteins for O60200 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O60200  Go to UniProtKB:  O60200

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein UPS1, mitochondrial	C	189	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UPS1, YLR193C
UniProt
Find proteins for Q05776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05776  Go to UniProtKB:  Q05776

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein UPS1, mitochondrial	G	189	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UPS1, YLR193C
UniProt
Find proteins for Q05776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05776  Go to UniProtKB:  Q05776

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial distribution and morphology protein 35	H	86	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MDM35, YKL053C-A
UniProt
Find proteins for O60200 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O60200  Go to UniProtKB:  O60200

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, E, I, K	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.311	α = 90
b = 130.736	β = 103.09
c = 84.271	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
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: 2024-11-20
  Changes: Data collection, Database references, Structure summary