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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.202 (Depositor), 0.213 (DCC)
R-Value Work:
0.164 (Depositor)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5JQM

This is version 1.3 of the entry. See complete history.

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	O60200 Q05776
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.202 (Depositor), 0.213 (DCC)
R-Value Work: 0.164 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.