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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 (130) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 528 557 3
Proteins 528 556 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 0.00006797 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.007677 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.01495 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.1072 Least Informative Inherited
Biological Process (BP) biological regulation 0.1316 Least Informative Inherited
Biological Process (BP) response to stimulus 0.8501 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.3801 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.007183 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01198 Least Informative Inherited
Biological Process (BP) immune system process 0.000002258 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0003766 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.1589 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.006867 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.02027 Moderately Informative Inherited
Biological Process (BP) response to stress 0.03589 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01404 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.3233 Moderately Informative Inherited
Biological Process (BP) system development 0.9494 Moderately Informative Inherited
Biological Process (BP) reproduction 0.01551 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.05305 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.05689 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.03745 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.009299 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.00001487 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.000005079 Informative Direct
Biological Process (BP) microtubule-based process 0.00000001915 Informative Direct
Biological Process (BP) cell cycle process 0.0000003803 Informative Direct
Biological Process (BP) regulation of organelle organization 0.000003377 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.000004456 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0003769 Informative Direct
Biological Process (BP) regulation of cell cycle 0.0001268 Informative Direct
Biological Process (BP) cytoskeleton organization 0.01947 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.01931 Informative Inherited
Biological Process (BP) microtubule cytoskeleton organization 0.000000001151 Highly Informative Direct
Biological Process (BP) aging 0.00002947 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0000002297 Highly Informative Direct
Biological Process (BP) hemopoiesis 0.00000000001433 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0000000007686 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.0000000004645 Highly Informative Direct
Molecular Function (MF) binding 0.001001 Least Informative Inherited
Molecular Function (MF) protein binding 0.05219 Moderately Informative Inherited
Molecular Function (MF) transcription factor binding 0.000000008067 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000002605 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000001834 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00000001104 Least Informative Direct
Cellular Component (CC) nuclear part 0.00000458 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000001045 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.7751 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.0000004215 Informative Direct
Cellular Component (CC) nucleolus 0.00000004117 Highly Informative Direct
Cellular Component (CC) centrosome 0.0001673 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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately 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)
Cellular componentNucleus0Least InformativeDirect
Molecular functionRNA-binding0.0002569Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationPhosphoprotein0.0000000007322Least InformativeDirect
Post-translational modificationAcetylation0.00000186Least 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 ]