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Helical domain of Sec23/24 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   ERP29 C domain-like [ 47932] (2)
Superfamily:   Helical domain of Sec23/24 [ 81811]
Families:   Helical domain of Sec23/24 [ 81812] (2)


Superfamily statistics
Genomes (494) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,514 2,642 4
Proteins 2,511 2,637 4


Functional annotation
General category Other
Detailed category Unknown function

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) localization 0.000000000004838 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0001885 Least Informative Direct
Biological Process (BP) biosynthetic process 0.3818 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.0377 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.6746 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1291 Least Informative Inherited
Biological Process (BP) developmental process 0.03184 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.4147 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.8977 Least Informative Inherited
Biological Process (BP) cellular localization 0.00000000000003449 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.000003908 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0002827 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0005335 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.001913 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.04456 Moderately Informative Inherited
Biological Process (BP) organ development 0.2902 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2425 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.03642 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.3591 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.001142 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.01383 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.06374 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01738 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.4739 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1628 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.08064 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.01598 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.01921 Moderately Informative Inherited
Biological Process (BP) positive regulation of transport 0.000001079 Informative Direct
Biological Process (BP) cellular membrane organization 0.000002055 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.000003498 Informative Direct
Biological Process (BP) tube development 0.00003746 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.00007929 Informative Direct
Biological Process (BP) protein transport 0.0001419 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0002868 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0005828 Informative Direct
Biological Process (BP) embryonic organ development 0.001735 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.0164 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1368 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.005338 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.003578 Informative Inherited
Biological Process (BP) muscle structure development 0.00352 Informative Inherited
Biological Process (BP) organelle localization 0.5069 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.01213 Informative Inherited
Biological Process (BP) regulation of secretion 0.01347 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.01614 Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.0000000000006402 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000001869 Highly Informative Direct
Biological Process (BP) post-translational protein modification 0.000000002282 Highly Informative Direct
Biological Process (BP) protein glycosylation 0.00000002045 Highly Informative Direct
Biological Process (BP) respiratory system development 0.00000002905 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.00000009995 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0.000001578 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.00001148 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.00001409 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.0001053 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0005086 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000007182 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00009018 Least Informative Direct
Cellular Component (CC) membrane 0.000822 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.003205 Least Informative Inherited
Cellular Component (CC) protein complex 0.003755 Least Informative Inherited
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.0000000000005442 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.0000003024 Moderately Informative Direct
Cellular Component (CC) coated vesicle 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0.00000009954 Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.00001164 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.00001951 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0Moderately InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)germline nuclear positioning variant0InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0InformativeDirect
Worm Phenotype (WP)germ cell compartment size variant0Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

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

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCytoplasm0.0000000596Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0004048Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006900 SSF81811 Protein matches
Abstract

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [PubMed11535824]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation [PubMed12239560].

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger , an alpha/beta trunk domain , an all-helical region, and a C-terminal gelsolin-like domain . This entry describes the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.


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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 Helical domain of Sec23/24 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 Helical domain of Sec23/24 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]