SUPERFAMILY 1.75 HMM library and genome assignments server


Transferrin receptor-like dimerisation domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   N-cbl like [ 47667] (5)
Superfamily:   Transferrin receptor-like dimerisation domain [ 47672]
Families:   Transferrin receptor-like dimerisation domain [ 47673] (2)


Superfamily statistics
Genomes (409) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,366 0 5
Proteins 1,342 0 5


Functional annotation
General category Processes_IC
Detailed category Transport

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) protein metabolic process 3.406e-06 Least Informative Direct
Biological Process (BP) localization 0.161 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6882 Least Informative Inherited
Biological Process (BP) homeostatic process 0.06529 Moderately Informative Inherited
Biological Process (BP) proteolysis 2.229e-09 Informative Direct
Biological Process (BP) cellular cation homeostasis 8.152e-08 Informative Direct
Biological Process (BP) metal ion homeostasis 6.744e-08 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.01178 Informative Inherited
Biological Process (BP) cellular transition metal ion homeostasis 8.065e-12 Highly Informative Direct
Biological Process (BP) iron ion homeostasis 2.277e-12 Highly Informative Direct
Molecular Function (MF) hydrolase activity 7.828e-05 Least Informative Direct
Molecular Function (MF) receptor activity 0.0004595 Informative Direct
Molecular Function (MF) peptidase activity 3.2e-12 Informative Direct
Molecular Function (MF) exopeptidase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0.003712 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7973 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.002168 Moderately Informative Inherited
Cellular Component (CC) endosome 6.971e-05 Informative Direct
Cellular Component (CC) integral to membrane 3.093e-09 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0Least InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details) Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processEndocytosis0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionZinc5.218e-10Least InformativeDirect
Molecular functionMetal-binding0.0009294Least InformativeDirect
Post-translational modificationHydrolase9.006e-06Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor4.432e-16Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationCarboxypeptidase1.978e-15Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPalmitate2.675e-15Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR007365 SSF47672 Protein matches
Abstract

This entry represents the dimerisation domain found in the transferrin receptor, as well as in a number of other proteins including glutamate carboxypeptidase II and N-acetylated-alpha-linked acidic dipeptidase like protein.

The transferrin receptor (TfR) assists iron uptake into vertebrate cells through a cycle of endo- and exocytosis of the iron transport protein transferrin (Tf). TfR binds iron-loaded (diferric) Tf at the cell surface and carries it to the endosome, where the iron dissociates from Tf. The apo-Tf remains bound to TfR until it reaches the cell surface, where apo-Tf is replaced by diferric Tf from the serum to begin the cycle again. Human TfR is a homodimeric type II transmembrane protein. The crystal structure of a TfR monomer reveals a 3-domain structure: a protease-like domain that closely resembles carboxy- and amino-peptidases; an apical domain consisting of a beta-sandwich; and a helical dimerisation domain. The dimerisation domain consists of a 4-helical bundle that makes contact with each of the three domains in the dimer partner [PubMed10531064].


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) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Enzyme Commission (EC) · 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 2 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 Transferrin receptor-like dimerisation 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 2 hidden Markov models representing the Transferrin receptor-like dimerisation 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) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]