SUPERFAMILY 1.75 HMM library and genome assignments server

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 (516) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,521 2,680 4
Proteins 2,518 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 0.000000005291 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000523 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.08547 Least Informative Inherited
Biological Process (BP) developmental process 0.09206 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2307 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3514 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3472 Least Informative Inherited
Biological Process (BP) regulation of localization 0.0000005102 Moderately Informative Direct
Biological Process (BP) cellular localization 0.000007812 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.00005802 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0005275 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0009454 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.03825 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.03864 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.5532 Moderately Informative Inherited
Biological Process (BP) organ development 0.01864 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.002368 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1413 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.366 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1331 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5455 Moderately Informative Inherited
Biological Process (BP) tube development 0.000000182 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0000008691 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000007398 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.00001531 Informative Direct
Biological Process (BP) embryonic organ development 0.00002955 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00005837 Informative Direct
Biological Process (BP) single-organism membrane organization 0.00006077 Informative Direct
Biological Process (BP) positive regulation of transport 0.00006993 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0001203 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0001819 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0002098 Informative Direct
Biological Process (BP) cell projection organization 0.0002579 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0002897 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0004452 Informative Direct
Biological Process (BP) muscle structure development 0.0006427 Informative Direct
Biological Process (BP) regulation of secretion 0.1085 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.01022 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.1085 Informative Inherited
Biological Process (BP) regulation of intracellular transport 0.09652 Informative Inherited
Biological Process (BP) organ morphogenesis 0.009506 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.02531 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.06341 Informative Inherited
Biological Process (BP) generation of neurons 0.002221 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.01885 Informative Inherited
Biological Process (BP) respiratory system development 0.00000000003435 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0000000003743 Highly Informative Direct
Biological Process (BP) vesicle organization 0.0000004385 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.0000005555 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000001768 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.000007748 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.00001288 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0001944 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000001851 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00002374 Least Informative Direct
Cellular Component (CC) protein complex 0.0008062 Least Informative Direct
Cellular Component (CC) membrane 0.003273 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.02958 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.00000000000000158 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000000000000003071 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.00004397 Moderately Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000000428 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.000001744 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)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0Moderately InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology 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 componentCytoplasm0.0000001376Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0003717Least 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 ]