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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 (129) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 527 557 3
Proteins 527 556 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 0.000000000002727 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.000004922 Least Informative Direct
Biological Process (BP) developmental process 0.0009683 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.006069 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01037 Least Informative Inherited
Biological Process (BP) localization 0.002848 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7716 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.003247 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.00367 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.006125 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.01196 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.0326 Least Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.000000000000005594 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.00000000001709 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000002535 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.000000006082 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.00000001128 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00000001597 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00001513 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00002735 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0001302 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0001374 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0001734 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0002895 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00042 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0005351 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.5427 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.1923 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.002436 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.0689 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.01772 Moderately Informative Inherited
Biological Process (BP) regulation of kinase activity 0 Informative Direct
Biological Process (BP) regulation of cell cycle process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.00000000000001264 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0000000000001566 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.00000000001092 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00000000219 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000000008223 Informative Direct
Biological Process (BP) growth 0.0000000128 Informative Direct
Biological Process (BP) nitrogen compound transport 0.00000002028 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.000000316 Informative Direct
Biological Process (BP) organelle localization 0.0000005815 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.000004237 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.000005882 Informative Direct
Biological Process (BP) microtubule-based process 0.000006965 Informative Direct
Biological Process (BP) cell cycle process 0.0000597 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001392 Informative Direct
Biological Process (BP) cytoskeleton organization 0.06416 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.005436 Informative Inherited
Biological Process (BP) chromosome organization 0.2488 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.003369 Informative Inherited
Biological Process (BP) establishment of RNA localization 0 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.0000000000002463 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000000002854 Highly Informative Direct
Biological Process (BP) regulation of mRNA processing 0.0000000000006344 Highly Informative Direct
Biological Process (BP) cell growth 0.00000000004646 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.0000000002987 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.00000001512 Highly Informative Direct
Biological Process (BP) nuclear export 0.00000008718 Highly Informative Direct
Biological Process (BP) aging 0.0000004574 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0002211 Highly Informative Direct
Molecular Function (MF) binding 0.000000001017 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000000005553 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.000009105 Informative Direct
Molecular Function (MF) unfolded protein binding 0.00000000001004 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00000003906 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000002043 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.00000009048 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000001119 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.7619 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.0000000398 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000002282 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000672 Moderately Informative Direct
Cellular Component (CC) cytosol 0.0001111 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.009474 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0358 Informative Inherited
Cellular Component (CC) nuclear body 0 Highly Informative Direct
Cellular Component (CC) centrosome 0.000000000003494 Highly Informative Direct
Cellular Component (CC) nucleolar part 0.00000000001005 Highly Informative Direct

Document: GO 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)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentNucleus0Least InformativeDirect
Molecular functionRNA-binding0.00008616Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationPhosphoprotein0.000000000003688Least InformativeDirect
Post-translational modificationAcetylation0.000002348Least 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) · 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) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]