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Nucleoplasmin-like core domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Nucleoplasmin-like/VP (viral coat and capsid proteins) [ 88632] (7)
Superfamily:   Nucleoplasmin-like core domain [ 69203]
Families:   Nucleoplasmin-like core domain [ 69204] (3)


Superfamily statistics
Genomes (133) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 533 975 3
Proteins 533 971 3


Functional annotation
General category Information
Detailed category Chromatin structure

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular component organization or biogenesis 0.0001337 Least Informative Direct
Biological Process (BP) primary metabolic process 0.4519 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01519 Least Informative Inherited
Biological Process (BP) biological regulation 0.2046 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9301 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.009681 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.1316 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.008984 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.0186 Least Informative Inherited
Biological Process (BP) immune system process 0.000006457 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0008655 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0003906 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.1696 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01463 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.006199 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02806 Moderately Informative Inherited
Biological Process (BP) reproduction 0.004865 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.0545 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.05886 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.001365 Moderately Informative Inherited
Biological Process (BP) system development 0.9356 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.00001514 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.000009101 Informative Direct
Biological Process (BP) microtubule-based process 0.00000007548 Informative Direct
Biological Process (BP) cell cycle process 0.000006722 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00001576 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.000004003 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.00005064 Informative Direct
Biological Process (BP) regulation of cell cycle 0.0001471 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.01903 Informative Inherited
Biological Process (BP) single organism reproductive process 0.02255 Informative Inherited
Biological Process (BP) chromosome organization 0.1208 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.03518 Informative Inherited
Biological Process (BP) microtubule cytoskeleton organization 0.000000001149 Highly Informative Direct
Biological Process (BP) aging 0.00003899 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0000002047 Highly Informative Direct
Biological Process (BP) fertilization 0.0000001696 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000001361 Highly Informative Direct
Molecular Function (MF) binding 0.0007726 Least Informative Direct
Molecular Function (MF) transcription factor binding 0.000000007686 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000002478 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000135 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000000002908 Least Informative Direct
Cellular Component (CC) nuclear part 0.000001113 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000001597 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.57 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02384 Informative Inherited
Cellular Component (CC) microtubule organizing center 0.000000002041 Highly Informative Direct

Document: GO annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processFertilization0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Post-translational modificationDevelopmental protein0.0000002319Moderately InformativeDirect
Post-translational modificationRNA-binding0.0002375Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationChromatin regulator0.0000000004226InformativeDirect
Post-translational modificationPhosphoprotein0.0000000007241Least InformativeDirect
Post-translational modificationAcetylation0.000001922Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR004301 SSF69203 Protein matches
Abstract Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays.

InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 3 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Nucleoplasmin-like core domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 3 hidden Markov models representing the Nucleoplasmin-like core domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]