5DQQ | pdb_00005dqq

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb5DQQ/pdb

• Classification: TRANSPORT PROTEIN/INHIBITOR
• Organism(s): Arabidopsis thaliana
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-09-15 Released: 2016-03-09 
• Deposition Author(s): Kintzer, A.F., Stroud, R.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.339 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.297 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.299 (Depositor) 

Literature

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana

Kintzer, A.F., Stroud, R.M.

(2016) Nature 531: 258-262

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 84.9 kDa 
• Atom Count: 5,402 
• Modeled Residue Count: 649 
• Deposited Residue Count: 723 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two pore calcium channel protein 1	A	723	Arabidopsis thaliana	Mutation(s): 0  Gene Names: TPC1, CCH1, FOU2, At4g03560, F9H3.19, T5L23.5 Membrane Entity: Yes
UniProt
Find proteins for Q94KI8 (Arabidopsis thaliana) Explore Q94KI8  Go to UniProtKB:  Q94KI8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
66R	J [auth A]	trans-Ned 19 C30 H31 F N4 O3 FUHCEERDBRGPQZ-LBNVMWSVSA-N
PLM	I [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.339 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.297 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.299 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.18	α = 90
b = 154.81	β = 90
c = 219.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHARP	phasing
DM	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Kintzer, A.F., Stroud, R.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM24485

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Structure summary