8D00

Structure of the Arabidopsis thaliana SPIRAL2 TOG domain

PDB DOI: https://doi.org/10.2210/pdb8D00/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-25 Released: 2023-11-29
Deposition Author(s): Slep, K.C., Bolhuis, D.L.
Funding Organization(s): University of North Carolina Ralph W. Mosley Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259
R-Value Work: 0.214
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A structurally divergent TOG domain stabilizes microtubule minus ends in Arabidopsis

Fan, Y., Bilkey, N., Bolhuis, D.L., Slep, K.C., Dixit, R.

(2023) Plant Cell

Macromolecule Content

Total Structure Weight: 33.05 kDa
Atom Count: 2,264
Modelled Residue Count: 299
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated protein TORTIFOLIA1	A	305	Arabidopsis thaliana	Mutation(s): 0 Gene Names: TOR1, CN, SPR2, At4g27060, T24A18.10
UniProt
Find proteins for Q9T041 (Arabidopsis thaliana) Explore Q9T041 Go to UniProtKB: Q9T041
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9T041
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259
R-Value Work: 0.214
R-Value Observed: 0.218
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.843	α = 90
b = 78.456	β = 90
c = 131.938	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
University of North Carolina Ralph W. Mosley Fund	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release

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 R01GM133198.