SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (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) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.00000000000008954 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000000008912 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000004592 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000000006337 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002497 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000001164 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00000488 Least Informative Direct
Biological Process (BP) localization 0.0000367 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.1171 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.006074 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1205 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.00000000002521 Moderately Informative Direct
Biological Process (BP) system process 0.00000000005599 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0000000001279 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.000000001413 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.000000003133 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.000000005514 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000000007333 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.0000001167 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00001377 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.00002157 Moderately Informative Direct
Biological Process (BP) tissue development 0.9901 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6102 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2535 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.6706 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.709 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.00247 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.002455 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.06862 Moderately Informative Inherited
Biological Process (BP) organ development 0.4919 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 0 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) synaptic transmission 0 Informative Direct
Biological Process (BP) regulation of kinase activity 0 Informative Direct
Biological Process (BP) single-organism behavior 0 Informative Direct
Biological Process (BP) alcohol metabolic process 0 Informative Direct
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) regulation of mitotic cell cycle 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 0.000000000000003755 Informative Direct
Biological Process (BP) generation of neurons 0.000000000000007347 Informative Direct
Biological Process (BP) phosphorylation 0.00000000000001435 Informative Direct
Biological Process (BP) locomotion 0.0000000000003881 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000000000005458 Informative Direct
Biological Process (BP) microtubule-based process 0.000000000001404 Informative Direct
Biological Process (BP) cell projection organization 0.00000000009314 Informative Direct
Biological Process (BP) regulation of growth 0.0000000003559 Informative Direct
Biological Process (BP) central nervous system development 0.0000000007992 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000001611 Informative Direct
Biological Process (BP) cellular component movement 0.0000002014 Informative Direct
Biological Process (BP) apoptotic process 0.0000002103 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.00000125 Informative Direct
Biological Process (BP) regulation of nervous system development 0.000009995 Informative Direct
Biological Process (BP) response to oxidative stress 0.00002095 Informative Direct
Biological Process (BP) regulation of cell development 0.00002514 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.00003237 Informative Direct
Biological Process (BP) muscle tissue development 0.000182 Informative Direct
Biological Process (BP) regulation of cell cycle process 1 Informative Inherited
Biological Process (BP) muscle structure development 0.05186 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.001505 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.002413 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.711 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.8455 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.9817 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) cytoskeleton-dependent intracellular transport 0 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) adult behavior 0 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0 Highly Informative Direct
Biological Process (BP) cell growth 0 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 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) regulation of multicellular organism growth 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) cell-type specific apoptotic process 0.0000000000003033 Highly Informative Direct
Biological Process (BP) chemotaxis 0.000000000001088 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00000000002197 Highly Informative Direct
Biological Process (BP) neuromuscular process 0.0000000004004 Highly Informative Direct
Biological Process (BP) muscle fiber development 0.0000000005611 Highly Informative Direct
Biological Process (BP) developmental growth 0.0000000008549 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.00000003028 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.0000002474 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.000006462 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00001608 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.0006902 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 1 Highly Informative Inherited
Biological Process (BP) learning or memory 0.005128 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.006633 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000000002967 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.00000000000007025 Informative Direct
Cellular Component (CC) membrane 0.000000001892 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00001802 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8272 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.549 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1029 Least Informative Inherited
Cellular Component (CC) protein complex 0.04524 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.000000000000006088 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00000000000003157 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000001065 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.0009551 Moderately Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) neuron projection 0 Informative Direct
Cellular Component (CC) integral to membrane 0.000000000000001589 Informative Direct
Cellular Component (CC) cell junction 0.00001924 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.0000296 Informative Direct
Cellular Component (CC) coated vesicle 0.0004135 Informative Direct
Cellular Component (CC) cilium part 0.0000000001785 Highly Informative Direct
Cellular Component (CC) spindle 0.00000002651 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000000207 Highly Informative Direct
Cellular Component (CC) transport vesicle 0.0001228 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least 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 splicing0.000000000007916Least 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 ]