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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 (517) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,524 2,680 4
Proteins 2,521 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) cellular component organization or biogenesis 0.0002195 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.06474 Least Informative Inherited
Biological Process (BP) biological regulation 0.2957 Least Informative Inherited
Biological Process (BP) regulation of localization 0.000007876 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.00009573 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000005744 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.3721 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.4925 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.9927 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.05128 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.003266 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.003256 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.02606 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.001262 Moderately Informative Inherited
Biological Process (BP) system development 0.5444 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.001294 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.01164 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8999 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.008306 Moderately Informative Inherited
Biological Process (BP) embryo development 0.000008796 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.000000002404 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0000007693 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0000005248 Informative Direct
Biological Process (BP) single-organism membrane organization 0.0002609 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0005837 Informative Direct
Biological Process (BP) positive regulation of transport 0.0004507 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.01378 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.1883 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.001875 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.01124 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.02448 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.001657 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.003752 Informative Inherited
Biological Process (BP) protein targeting 0.1956 Informative Inherited
Biological Process (BP) regulation of secretion 0.1767 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.001227 Informative Inherited
Biological Process (BP) establishment or maintenance of cell polarity 0.00001671 Highly Informative Direct
Biological Process (BP) regulation of cell shape 0.0000256 Highly Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0000000000009541 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0.00008896 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000001304 Highly Informative Direct
Biological Process (BP) cell projection organization 0.0003521 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000002549 Highly Informative Direct
Biological Process (BP) tube morphogenesis 0.000004933 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0.000005984 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.000000001844 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.00000000009014 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000000001233 Highly Informative Direct
Biological Process (BP) establishment of protein localization to membrane 0.0002868 Highly Informative Direct
Biological Process (BP) vesicle-mediated transport to the plasma membrane 0.0009471 Highly Informative Direct
Biological Process (BP) muscle structure development 0.004558 Highly Informative Inherited
Molecular Function (MF) molecular function regulator 0.002074 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 0.00000707 Informative Direct
Molecular Function (MF) GTPase regulator activity 0.0000004932 Highly Informative Direct
Cellular Component (CC) membrane 0.00000532 Least Informative Direct
Cellular Component (CC) protein complex 0.00000000004365 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000004661 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.003203 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000000007271 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.00000000000003408 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) whole membrane 0 Moderately Informative Direct
Cellular Component (CC) transport vesicle 0 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0 Informative Direct
Cellular Component (CC) vesicle membrane 0 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 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)larval lethal0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0Least InformativeDirect
Worm Phenotype (WP)cell development variant0Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least 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 component morphology variant0Moderately InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0InformativeDirect
Worm Phenotype (WP)organelle organization biogenesis 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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)kidney0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least 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)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least 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.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral 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 componentCytoplasm0.0000001045Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0005035Least 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) · Xenopus Anatomy (XA) · 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]