Data pertaining to structural and functional analyses of NF-kB in diverse holozoan taxa

Published Mar 07, 2026 on Dryad. https://doi.org/10.5061/dryad.t1g1jwtfx

Data files

Mar 07, 2026 version files 57.97 KB

Abstract

This repository contains data pertaining to sequence and structural analyses of the transcription factor NF-kB across a diverse set of holozoan species. Dataset includes data relevant to comparative sequence analyses of the NF-kB Rel homology domain (RHD), as well as comparative analyses of three-dimensional structures of this domain predicted using AlphaFold3. Further, data are included for an analysis correlating NF-kB RHD sequence and structural similarity between species with binding preference as previously quantified using protein binding microarrays (PBMs). All data are available for open use.

Dataset DOI: 10.5061/dryad.t1g1jwtfx

Data and file structure

File 1: NFkB_sequences.fa

This file contains amino acid sequences in FASTA format for the NF-kB proteins analyzed.

File 2: PBM_correlation_data.csv

This file is for data pertaining to NF-kB binding specificity (as determined via protein binding microarrays [PBM]) and structural features (amino acid percent identity or root mean square deviation (RMSD)).

This file has headers, which are:
-Species_pair = the pair of species for which NF-kB proteins were compared; abbreviations are 4 letters with the first letter indicating genus and the next 3 letters indicating the first 3 letters of the species name (e.g., Mvir = Morbakka virulenta)
-PBM_z_score = correlation of z-scores from protein binding microarray (PBM)
-Structure_metric = structural metric analyzed (either amino acid percent identity or RMSD)
-Structure_value = value for metric identified in "Structure_metric"

File 3: RHD_PCA_data.csv

This file is for data pertaining to a principle components analysis (PCA) performed on substitution matrix scores from a multiple sequence alignment of Rel homology domain (RHD) sequences from NF-kB proteins.

This file has headers, which are:
-Sequence = species of origin for RHD sequence; abbreviations are 4 letters with the first letter indicating genus and the next 3 letters indicating the first 3 letters of the species name (e.g., Mvir = Morbakka virulenta)
-PC1–3 = first through third PC values

File 4: RHD_percent_identity_data.csv

This file is for data pertaining to the percent amino acid identities from pairwise sequence alignments for NF-kBs from pairs of species

This file has headers, which are:
-Species_1–2 = species being compared; abbreviations are 4 letters with the first letter indicating genus and the next 3 letters indicating the first 3 letters of the species name (e.g., Mvir = Morbakka virulenta)
-Percent_identity = percentage of amino acid identities

File 5: RHD_sequences.fa

This file contains amino acid sequences in FASTA format for the Rel homology domains of the NF-kB proteins analyzed.

File 6: RMSD_data.csv

This file is for data pertaining to root mean square deviations between predicted NF-kB structures generated via AlphaFold3

This file has headers, which are:
-Species_1–2 = species being compared; abbreviations are 4 letters with the first letter indicating genus and the next 3 letters indicating the first 3 letters of the species name (e.g., Mvir = Morbakka virulenta)
-RMSD = root mean square deviation between sequences calculated using PyMOL

File 7: RHD_MSA.aln-clustal_num

This file contains the multiple sequence alignment (MSA) of the Rel homology domain (RHD) sequences in in CLUSTAL format with residue numbering

Sharing/Access information

Links to other publicly accessible locations of the data:

Data was derived from the following sources:

PBM data originally from Mansfield et al. (2017) Scientific Reports

Code/Software

File 1: NFkB_review_code.Rmd

This file contains code in R markdown format for the reproduction of all analyses and figure generation. Code can be run using the CSV files in this repository.