SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (135) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 536 975 3
Proteins 536 971 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) multicellular organismal process 0.0000199 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0004804 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0217 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.1756 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.5404 Least Informative Inherited
Biological Process (BP) biological regulation 0.3602 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.02634 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01304 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01397 Least Informative Inherited
Biological Process (BP) immune system process 0.00000002435 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0003401 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.1623 Moderately Informative Inherited
Biological Process (BP) reproduction 0.007866 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01479 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.01017 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.04705 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.04481 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.05448 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.001232 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.001371 Moderately Informative Inherited
Biological Process (BP) hemopoiesis 0.000000000000001925 Informative Direct
Biological Process (BP) microtubule-based process 0.00000007808 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.000004183 Informative Direct
Biological Process (BP) cell cycle process 0.000005911 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00001307 Informative Direct
Biological Process (BP) DNA metabolic process 0.00002226 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00002616 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.00009032 Informative Direct
Biological Process (BP) regulation of cell cycle 0.0001336 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.01875 Informative Inherited
Biological Process (BP) single organism reproductive process 0.03719 Informative Inherited
Biological Process (BP) chromosome organization 0.1193 Informative Inherited
Biological Process (BP) positive regulation of cell cycle process 0.00000000186 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000002089 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.000000002638 Highly Informative Direct
Biological Process (BP) fertilization 0.0000001642 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.000000209 Highly Informative Direct
Biological Process (BP) aging 0.00008864 Highly Informative Direct
Molecular Function (MF) binding 0.003574 Least Informative Inherited
Molecular Function (MF) transcription factor binding 0.000000008172 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000003121 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.00000000007545 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000000002007 Least Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000000002231 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.00000007249 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.8465 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02051 Informative Inherited
Cellular Component (CC) microtubule organizing center 0.000000003609 Highly Informative Direct

Document: GO 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 protein0.0000002314Moderately InformativeDirect
Post-translational modificationRNA-binding0.0002336Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationChromatin regulator0.0000000004196InformativeDirect
Post-translational modificationPhosphoprotein0.0000000007714Least InformativeDirect
Post-translational modificationAcetylation0.000001837Least 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]