8DTF | pdb_00008dtf

Cryo-EM structure of the full length Arabidopsis SPY with complete TPRs

PDB DOI: https://doi.org/10.2210/pdb8DTF/pdb
EM Map EMD-27696: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-07-25 Released: 2023-03-08
Deposition Author(s): Kumar, S., Zhou, Y., Dillard, L., Borgnia, M.J., Bartesaghi, A., Zhou, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the full length Arabidopsis SPY with complete TPRs

Kumar, S., Zhou, Y.

(2023) Nat Commun

Macromolecule Content

Total Structure Weight: 210.56 kDa
Atom Count: 12,414
Modeled Residue Count: 1,606
Deposited Residue Count: 1,892
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY	A, B	946	Arabidopsis thaliana	Mutation(s): 0 Gene Names: SPY, At3g11540, F24K9.29 EC: 2.4.1.255 (PDB Primary Data), 2.4.1.221 (PDB Primary Data)
UniProt
Find proteins for Q96301 (Arabidopsis thaliana) Explore Q96301 Go to UniProtKB: Q96301
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96301
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection

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.