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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 (515) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,517 2,680 4
Proteins 2,514 2,679 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 0.000000003004 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0003647 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.3289 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2767 Least Informative Inherited
Biological Process (BP) developmental process 0.09059 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.008638 Least Informative Inherited
Biological Process (BP) cellular localization 0.0000000001418 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0000003843 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0000367 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0005126 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0008627 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.5685 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1966 Moderately Informative Inherited
Biological Process (BP) organ development 0.02079 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.003299 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.3572 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1244 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1186 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.4189 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1431 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.001539 Moderately Informative Inherited
Biological Process (BP) tube development 0.00000002738 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0000008983 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000005872 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.00001407 Informative Direct
Biological Process (BP) positive regulation of transport 0.00003852 Informative Direct
Biological Process (BP) embryonic organ development 0.00007574 Informative Direct
Biological Process (BP) cellular membrane organization 0.0001096 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0001728 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0001774 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0001803 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0001854 Informative Direct
Biological Process (BP) protein transport 0.0008364 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.1025 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.00127 Informative Inherited
Biological Process (BP) organ morphogenesis 0.02137 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.008903 Informative Inherited
Biological Process (BP) generation of neurons 0.002143 Informative Inherited
Biological Process (BP) muscle structure development 0.001539 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.01162 Informative Inherited
Biological Process (BP) regulation of secretion 0.1034 Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.00000000001545 Highly Informative Direct
Biological Process (BP) respiratory system development 0.00000000003438 Highly Informative Direct
Biological Process (BP) vesicle organization 0.0000004 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.0000005566 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000001811 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.00001168 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.00006931 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0009621 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000001304 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00004019 Least Informative Direct
Cellular Component (CC) protein complex 0.0008708 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.03437 Least Informative Inherited
Cellular Component (CC) membrane 0.003097 Least Informative Inherited
Cellular Component (CC) vesicle 0.000000000000003092 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.00000000000003157 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.000000000009261 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.00003641 Moderately Informative Direct
Cellular Component (CC) coated vesicle 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0.00008555 Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000003962 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.000007513 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)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)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCytoplasm0.0000001391Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0003672Least 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) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]