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 (458) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,401 1,526 4
Proteins 1,389 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 0.00000001527 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000008154 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.09566 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.664 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6199 Least Informative Inherited
Biological Process (BP) developmental process 0.02859 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2474 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.06703 Least Informative Inherited
Biological Process (BP) localization 0.2643 Least Informative Inherited
Biological Process (BP) regulation of localization 0.0008522 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00002796 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.0000001029 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.08079 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.002639 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.00000003912 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0003345 Informative Direct
Biological Process (BP) pigment metabolic process 0.00000000002552 Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.000000002259 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.000682 Informative Direct
Biological Process (BP) regulation of ion transport 0.001467 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.003696 Informative Inherited
Biological Process (BP) protein folding 0.000000000002447 Highly Informative Direct
Biological Process (BP) response to heat 0.00000002469 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0000000046 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0000001094 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 0.000000001801 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.00000000002106 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 0.00000000001477 Highly Informative Direct
Molecular Function (MF) binding 0.0000309 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 0.00000000000611 Highly Informative Direct
Cellular Component (CC) membrane 0.00002322 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000005704 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.001504 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00746 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.000000007142 Moderately Informative Direct
Cellular Component (CC) membrane region 0.0004125 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.1475 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.9911 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.00002101 Informative Direct
Cellular Component (CC) integral component of membrane 0.09516 Informative Inherited
Cellular Component (CC) integral component of organelle membrane 0.00002077 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000004964 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
DomainTransmembrane0.3217Least InformativeInherited
Molecular functionZinc0.000000000000001834Least InformativeDirect
Molecular functionMetal-binding0.000000000000007498Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionLectin0InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.0003924Least InformativeDirect
Post-translational modificationPalmitate0.000006807Moderately 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 ]