SUPERFAMILY 1.75 HMM library and genome assignments server

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 (122) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 379 462 1
Proteins 379 461 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) developmental process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0000000000001132 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000000009062 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000005668 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000000007819 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002574 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.00000229 Least Informative Direct
Biological Process (BP) localization 0.00004741 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0001796 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.5228 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1231 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.006067 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.09998 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) reproductive process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000000000000226 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.00000000005349 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.00000000007821 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00000000009149 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.0000000001611 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.000000001446 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.000000002383 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000000008571 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00000001115 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.00000008677 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000222 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.5901 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3627 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6102 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.06837 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.4613 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.001292 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.002366 Moderately Informative Inherited
Biological Process (BP) organ development 0.4571 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.002443 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) alcohol metabolic process 0 Informative Direct
Biological Process (BP) single-organism behavior 0 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) neurological system process 0 Informative Direct
Biological Process (BP) sexual reproduction 0 Informative Direct
Biological Process (BP) regulation of mitotic cell cycle 0 Informative Direct
Biological Process (BP) RNA processing 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0 Informative Direct
Biological Process (BP) growth 0.000000000000003707 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.000000000000003707 Informative Direct
Biological Process (BP) generation of neurons 0.000000000000007248 Informative Direct
Biological Process (BP) phosphorylation 0.00000000000009141 Informative Direct
Biological Process (BP) microtubule-based process 0.0000000000002434 Informative Direct
Biological Process (BP) locomotion 0.0000000000003788 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000000000005694 Informative Direct
Biological Process (BP) synaptic transmission 0.000000000008277 Informative Direct
Biological Process (BP) cell projection organization 0.00000000001003 Informative Direct
Biological Process (BP) regulation of growth 0.0000000002597 Informative Direct
Biological Process (BP) central nervous system development 0.00000000104 Informative Direct
Biological Process (BP) cellular component movement 0.00000003811 Informative Direct
Biological Process (BP) apoptotic process 0.000000209 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.000007161 Informative Direct
Biological Process (BP) regulation of nervous system development 0.00001021 Informative Direct
Biological Process (BP) regulation of cell development 0.00001451 Informative Direct
Biological Process (BP) response to oxidative stress 0.00002303 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0001614 Informative Direct
Biological Process (BP) regulation of cell cycle process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.8637 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.0205 Informative Inherited
Biological Process (BP) positive regulation of RNA metabolic process 0.001748 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.8179 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.00156 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.6585 Informative Inherited
Biological Process (BP) regulation of multicellular organism growth 0 Highly Informative Direct
Biological Process (BP) neuron projection development 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) positive regulation of mitotic cell cycle 0 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) regulation of peptidyl-tyrosine phosphorylation 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) learning or memory 0 Highly Informative Direct
Biological Process (BP) cell growth 0 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0 Highly Informative Direct
Biological Process (BP) cell recognition 0 Highly Informative Direct
Biological Process (BP) adult behavior 0.000000000000001913 Highly Informative Direct
Biological Process (BP) cell-type specific apoptotic process 0.0000000000003407 Highly Informative Direct
Biological Process (BP) chemotaxis 0.000000000001057 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00000000004111 Highly Informative Direct
Biological Process (BP) developmental growth 0.00000000007794 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.0000000001607 Highly Informative Direct
Biological Process (BP) negative regulation of nervous system development 0.00000001299 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.0000001909 Highly Informative Direct
Biological Process (BP) neuromuscular process 0.0000005583 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.000004548 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00008925 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-templated 0.007413 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 1 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000000008449 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0000000000000746 Informative Direct
Cellular Component (CC) membrane 0.000000001902 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00002119 Least Informative Direct
Cellular Component (CC) protein complex 0.04375 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.8071 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.07092 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.5565 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.000000000000007503 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00000000000004498 Moderately Informative Direct
Cellular Component (CC) vesicle 0.00000114 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.001143 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) integral component of membrane 0.000000000000003071 Informative Direct
Cellular Component (CC) synapse 0.0000000195 Informative Direct
Cellular Component (CC) cell junction 0.00001893 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.00003135 Informative Direct
Cellular Component (CC) ciliary part 0.000000001688 Highly Informative Direct
Cellular Component (CC) spindle 0.00000002789 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000002091 Highly Informative Direct
Cellular Component (CC) transport vesicle 0.00001049 Highly Informative Direct
Cellular Component (CC) coated vesicle 0.0001057 Highly 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 phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)decreased body size0InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0InformativeDirect

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune 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 splicing0.000000000007916Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionZinc0.0000000631Least InformativeDirect
Molecular functionMetal-binding0.00003869Least InformativeDirect
Molecular functionIron0.000001031Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.00002357Least InformativeDirect
Post-translational modificationProteoglycan0.0000000004177InformativeDirect

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 ]