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Zn-finger domain of Sec23/24 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Zn-finger domain of Sec23/24 [ 82919]
Families:   Zn-finger domain of Sec23/24 [ 82920] (2)


Superfamily statistics
Genomes (522) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,559 6,325 4
Proteins 2,556 6,316 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) cellular component organization or biogenesis 0.0000000008007 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00009198 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0003593 Least Informative Direct
Biological Process (BP) biological regulation 0.4087 Least Informative Inherited
Biological Process (BP) cellular localization 0.00000000000003598 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0000009933 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.00001589 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00002039 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.00006369 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0003278 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0003643 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0009015 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.2162 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.004917 Moderately Informative Inherited
Biological Process (BP) tissue development 0.08102 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.00228 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.00167 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.02496 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.7372 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.5942 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1696 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.002427 Moderately Informative Inherited
Biological Process (BP) intracellular transport 0.00000000007935 Informative Direct
Biological Process (BP) single-organism cellular localization 0.000000000373 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.000000006055 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00000001918 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.00000002756 Informative Direct
Biological Process (BP) protein transport 0.000001881 Informative Direct
Biological Process (BP) embryo development 0.00001093 Informative Direct
Biological Process (BP) positive regulation of transport 0.00001792 Informative Direct
Biological Process (BP) single-organism membrane organization 0.00005861 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.00008071 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.000199 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.0002919 Informative Direct
Biological Process (BP) regulation of cellular localization 0.0003015 Informative Direct
Biological Process (BP) generation of neurons 0.000325 Informative Direct
Biological Process (BP) hemopoiesis 0.0003422 Informative Direct
Biological Process (BP) animal organ morphogenesis 0.0006875 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.001119 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.001626 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.003327 Informative Inherited
Biological Process (BP) cell development 0.00132 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.00331 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.03158 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.002565 Informative Inherited
Biological Process (BP) regulation of secretion 0.07432 Informative Inherited
Biological Process (BP) post-embryonic development 0.0741 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.005021 Informative Inherited
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000000000006427 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.0000000002885 Highly Informative Direct
Biological Process (BP) positive regulation of secretion by cell 0.000000000744 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0.00000003432 Highly Informative Direct
Biological Process (BP) embryonic organ development 0.0000000789 Highly Informative Direct
Biological Process (BP) regulation of GTPase activity 0.00000009416 Highly Informative Direct
Biological Process (BP) regulation of cell shape 0.0000001292 Highly Informative Direct
Biological Process (BP) tube morphogenesis 0.0000003725 Highly Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.000002685 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.000004497 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.000007898 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.00001258 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0.00004912 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.00005649 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.00007227 Highly Informative Direct
Biological Process (BP) myeloid cell differentiation 0.0001449 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0002207 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.01044 Highly Informative Inherited
Biological Process (BP) positive regulation of nervous system development 0.02618 Highly Informative Inherited
Biological Process (BP) neuron development 0.06375 Highly Informative Inherited
Molecular Function (MF) binding 0.004106 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.000009398 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.0001163 Moderately Informative Direct
Molecular Function (MF) zinc ion binding 0.0000000003496 Informative Direct
Molecular Function (MF) enzyme activator activity 0.00000005132 Informative Direct
Molecular Function (MF) amide binding 0.00003573 Informative Direct
Molecular Function (MF) GTPase regulator activity 0.00000000122 Highly Informative Direct
Molecular Function (MF) peptide binding 0.000001954 Highly Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000000007336 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000000135 Least Informative Direct
Cellular Component (CC) membrane 0.000000000529 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00001256 Least Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) whole membrane 0 Moderately Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0 Informative Direct
Cellular Component (CC) extrinsic component of membrane 0.0008755 Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0 Highly Informative Direct
Cellular Component (CC) membrane coat 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) Golgi subcompartment 1 Highly Informative Inherited

Document: GO 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 componentCytoplasm0Least InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0005207Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006895 SSF82919 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 an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex.

More information about these proteins can be found at Protein of the Month: Zinc Fingers.


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) · 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 Zn-finger 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 Zn-finger 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) · UniProtKB KeyWords (KW) · Internal database links ]