SUPERFAMILY 1.75 HMM library and genome assignments server


P-domain of calnexin/calreticulin superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   P-domain of calnexin/calreticulin [ 63886]
Superfamily:   P-domain of calnexin/calreticulin [ 63887]
Families:   P-domain of calnexin/calreticulin [ 63888] (2)


Superfamily statistics
Genomes (446) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,325 1,526 4
Proteins 1,315 1,520 4


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and 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 4.559e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.414e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.005096 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.6227 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.07123 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5201 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2924 Least Informative Inherited
Biological Process (BP) localization 0.2831 Least Informative Inherited
Biological Process (BP) developmental process 0.04256 Least Informative Inherited
Biological Process (BP) regulation of localization 0.0006974 Moderately Informative Direct
Biological Process (BP) cellular response to stress 4.347e-05 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.078 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.07643 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.002667 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 6.003e-08 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0003352 Informative Direct
Biological Process (BP) pigment metabolic process 4.783e-11 Informative Direct
Biological Process (BP) regulation of ion transport 0.001284 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.004839 Informative Inherited
Biological Process (BP) tissue homeostasis 7.43e-11 Highly Informative Direct
Biological Process (BP) protein folding 2.617e-12 Highly Informative Direct
Biological Process (BP) response to heat 2.369e-08 Highly Informative Direct
Biological Process (BP) regulation of protein stability 4.315e-09 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 8.778e-08 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 1.406e-09 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 1.85e-11 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 1.054e-10 Highly Informative Direct
Molecular Function (MF) binding 0.0001029 Least Informative Direct
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) calcium ion binding 0 Highly Informative Direct
Molecular Function (MF) unfolded protein binding 8.239e-12 Highly Informative Direct
Cellular Component (CC) membrane 5.035e-05 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 4.698e-10 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1.085e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.005608 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 1.9e-06 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.0001952 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.1623 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 2.408e-05 Informative Direct
Cellular Component (CC) integral to membrane 0.0002906 Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 3.192e-05 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 7.674e-07 Highly Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentSarcoplasmic reticulum0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.3192Least InformativeInherited
Molecular functionZinc1.84e-15Least InformativeDirect
Molecular functionMetal-binding5.478e-15Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionLectin0InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.0003961Least InformativeDirect
Post-translational modificationPalmitate6.818e-06Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009033 SSF63887 Protein matches
Abstract

The type-I integral membrane protein calnexin (CNX) and its soluble paralog calreticulin (CRT) are members of a family of molecular chaperones that function in the endoplasmic reticulum (ER) of eukaryotic cells. These calcium-binding proteins are lectins that bind newly synthesised N-linked glycoproteins to help promote efficient folding and oligomeric assembly. The chaperones act to retain the glycoproteins in the ER while they are still incompletely folded, ensuring that the ER quality control machinery can dispose of misfolded glycoproteins. The family of molecular chaperones are conserved among plants, fungi, and animals.

The P domain contains a high-affinity calcium-binding site and is thought to be involved in either substrate binding or protein-protein interactions. The P domain forms part of the lumenal region in CNX. In both CRT and CNX the P domain forms a protrusion, or arm, extending from the core protein. The amino acid sequence of the P domain is highly conserved and is characteristic for this family of lectins. The structure of the P domain consists of a non-globular proline-rich hairpin fold. The P domain is composed of multiple copies of two types of proline-rich repeat sequences, a 17 amino acid type 1 motif and a 14 amino acid type 2 motif, with the arrangement 111222 in CRT and 11112222 in CNX [PubMed11248044, PubMed11583625].


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) · Arabidopsis Plant Ontology (AP) · 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 P-domain of calnexin/calreticulin 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 P-domain of calnexin/calreticulin 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]