8D00 | pdb_00008d00

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 (Depositor), 0.260 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 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
Modeled 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] mmCIF 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 (Depositor), 0.260 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

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
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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.