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Amyloid beta a4 protein copper binding domain (domain 2) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Dodecin subunit-like [ 88797] (6)
Superfamily:   Amyloid beta a4 protein copper binding domain (domain 2) [ 89811]
Families:   Amyloid beta a4 protein copper binding domain (domain 2) [ 89812]


Superfamily statistics
Genomes (124) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 384 972 1
Proteins 384 970 1


Functional annotation
General category General
Detailed category Ion binding

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 0.000000002862 Least Informative Direct
Biological Process (BP) biological regulation 0.0000128 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00002787 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00003219 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00003734 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00009893 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.05587 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01694 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01875 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.005682 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.007197 Least Informative Inherited
Biological Process (BP) regulation of signaling 0.00000001568 Moderately Informative Direct
Biological Process (BP) single-organism transport 0.00000007531 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.00000008556 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0000001256 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0000001501 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000002043 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000004581 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000006901 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0000007697 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0000008602 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.000001023 Moderately Informative Direct
Biological Process (BP) gene expression 0.000001497 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000006088 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.000007446 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.00002621 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000534 Moderately Informative Direct
Biological Process (BP) cell communication 0.0001565 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.0002154 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0003708 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.009673 Moderately Informative Inherited
Biological Process (BP) system development 0.002099 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.4296 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.005573 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.07886 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.02367 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.04912 Moderately Informative Inherited
Biological Process (BP) growth 0 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000000000000007367 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.0000000000000109 Informative Direct
Biological Process (BP) ion homeostasis 0.00000000000003802 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00000000000007063 Informative Direct
Biological Process (BP) behavior 0.0000000000001264 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.000000000008069 Informative Direct
Biological Process (BP) microtubule-based process 0.00000000004303 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000000001228 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0000000001406 Informative Direct
Biological Process (BP) phosphorylation 0.000000002623 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.000000008118 Informative Direct
Biological Process (BP) central nervous system development 0.00000005062 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00000007289 Informative Direct
Biological Process (BP) locomotion 0.00000009009 Informative Direct
Biological Process (BP) regulation of growth 0.0000002005 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0000004871 Informative Direct
Biological Process (BP) regulation of cell cycle 0.000004646 Informative Direct
Biological Process (BP) response to radiation 0.0000329 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.00003591 Informative Direct
Biological Process (BP) system process 0.0001788 Informative Direct
Biological Process (BP) circulatory system development 0.0004575 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0004807 Informative Direct
Biological Process (BP) cell development 0.0005182 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.01691 Informative Inherited
Biological Process (BP) tissue development 0.1682 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.01983 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.00227 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.207 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) cell growth 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) neuron development 0 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) neurological system process 0.000000000000009171 Highly Informative Direct
Biological Process (BP) morphogenesis of an epithelium 0.0000000000001467 Highly Informative Direct
Biological Process (BP) developmental growth involved in morphogenesis 0.000000000001458 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.00000000005762 Highly Informative Direct
Biological Process (BP) cell maturation 0.0000000008511 Highly Informative Direct
Biological Process (BP) chemotaxis 0.000000003281 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00000006826 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.000009265 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.00001128 Highly Informative Direct
Molecular Function (MF) binding 0.0001013 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000001355 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.00000001012 Informative Direct
Cellular Component (CC) membrane 0.000143 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.002117 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.4095 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.000000000979 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000000002145 Moderately Informative Direct
Cellular Component (CC) vesicle 0.008866 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.000000000005693 Informative Direct
Cellular Component (CC) Golgi apparatus 0.00000000001155 Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body region phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0Moderately InformativeDirect
Mammalian Phenotype (MP)decreased body size0InformativeDirect

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processNotch signaling pathway0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Coding sequence diversityAlternative splicing0.00000000001087Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionZinc0.00000002852Least InformativeDirect
Molecular functionMetal-binding0.0000177Least InformativeDirect
Molecular functionIron0.0000008292Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Post-translational modificationHeparin-binding0InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationSerine protease inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.00001201Least InformativeDirect
Post-translational modificationIsopeptide bond0.00000004935Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000003001Moderately InformativeDirect
Post-translational modificationProteoglycan0.000000000009117InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011178 SSF89811 Protein matches
Abstract

This entry represents a copper-binding domain found within the extracellular domain, which is at the N-terminal of amyloidogenic glycoproteins such as amyloid-beta precursor protein (APP, or A4). The copper-binding domain has a dodecin-like fold consisting of a 2-layer alpha/beta topology [PubMed12611883].

More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein.


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) · Mouse Phenotype (MP) · 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 1 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 Amyloid beta a4 protein copper binding domain (domain 2) 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 1 hidden Markov models representing the Amyloid beta a4 protein copper binding domain (domain 2) 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) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]