5JQL | pdb_00005jql

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.248 (Depositor), 0.246 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 190.19 kDa
Atom Count: 11,018
Modeled Residue Count: 1,432
Deposited Residue Count: 1,650
Unique protein chains: 5

Macromolecules

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| 3D Structure

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

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| 3D Structure

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

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| 3D Structure

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

Find similar proteins by:

| 3D Structure

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

Find similar proteins by:

| 3D Structure

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

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.246 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

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

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View more in-depth experimental data

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: 2024-11-20
Changes: Data collection, Database references, Structure summary