8QSW

Bi-allelic variants of SPOUT1, a novel RNA methyltransferase, cause chromosome missegregation and a rare neurodevelopmental disease

PDB DOI: https://doi.org/10.2210/pdb8QSW/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-11 Released: 2024-10-23
Deposition Author(s): Jeyaprakash, A.A., Abad, M.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262
R-Value Work: 0.203
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Bi-allelic mutants of SPOUT1, a novel RNA methyltransferase, cause chromosome missegregation and a rare neurodevelopmental disease

Jeyaprakash, A.A., Abad, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 33.68 kDa
Atom Count: 2,205
Modelled Residue Count: 286
Deposited Residue Count: 307
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase C9orf114	A	307	Homo sapiens	Mutation(s): 0 Gene Names: SPOUT1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T280 (Homo sapiens) Explore Q5T280 Go to UniProtKB: Q5T280
PHAROS: Q5T280 GTEx: ENSG00000198917
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5T280
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.24	α = 90
b = 80.694	β = 90
c = 136.363	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

Jeyaprakash, A.A.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/X001245/1

Revision History (Full details and data files)

Version 1.0: 2024-10-23
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 R01GM157729.