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UniProtKB - P62323 (SMD3_XENLA)

Entry version 74 (02 Dec 2020)
Sequence version 1 (05 Jul 2004)
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Protein

Small nuclear ribonucleoprotein Sm D3

Gene

snrpd3

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Plays role in pre-mRNA splicing as core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes. Is also a component of the minor U12 spliceosome (By similarity). As part of the U7 snRNP it is involved in histone pre-mRNA 3'-end processing (By similarity).By similarity

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D3
Short name:
Sm-D3
Alternative name(s):
snRNP core protein D3
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:snrpd3
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiXenopus laevis (African clawed frog)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri8355 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus

Organism-specific databases

Xenopus laevis and tropicalis biology and genomics resource

More...Xenbasei		XB-GENE-1014508, snrpd3.L

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001222161 – 126Small nuclear ribonucleoprotein Sm D3Add BLAST126

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs.By similarity

Keywords - PTMi

Methylation

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P62323

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Most spliceosomal snRNPs contain a common set of Sm proteins, snrpb, snrpd1, snrpd2, snrpd3, snrpe, snrpf and snrpg that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP.

Component of the U1 snRNP. The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins snrpb, snrpd1, snrpd2, snrpd3, snrpe, snrpf and snrpg, and at least three U1 snRNP-specific proteins snrnp70/U1-70K, snrpa/U1-A and snrpc/U1-C.

Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least prpf3, prpf4, prpf6, prpf8, prpf31, snrnp200, txnl4a, snrnp40, snrpb, snrpd1, snrpd2, snrpd3, snrpe, snrpf, snrpg, ddx23, cd2bp2, ppih, snu13, eftud2, sart1 and usp39, plus lsm2, lsm3, lsm4, lsm5, lsm6, lsm7 and lsm8.

Component of the U7 snRNP complex, or U7 Sm protein core complex, that is composed of the U7 snRNA and at least lsm10, lsm11, snrpb, snrpd3, snrpe, snrpf and snrpg; the complex does not contain snrpd1 and snrpd2.

Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Part of the SMN-Sm complex that contains smn1, gemin2/sip1, ddx20/gemin3, gemin4, gemin5, gemin6, gemin7, gemin8, strap/unrip and the Sm proteins snrpb, snrpd1, snrpd2, snrpd3, snrpe, snrpf and snrpg; catalyzes core snRNPs assembly.

Forms a 6S pICln-Sm complex composed of clns1a/pICln, snrpd1, snrpd2, snrpe, snrpf and snrpg; ring-like structure where clns1a/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP.

By similarity

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P62323

Database of comparative protein structure models

More...ModBasei		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>Repeati110 – 11112
Repeati112 – 11322
Repeati114 – 11532
Repeati116 – 11742
Repeati118 – 11952

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni110 – 1195 X 2 AA tandem repeats of [RM]-G10

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi84 – 126Arg/Lys-rich (basic)Add BLAST43

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

Identification of Orthologs from Complete Genome Data

More...OMAi		HESLGHV

Database of Orthologous Groups

More...OrthoDBi		1584810at2759

Family and domain databases

Conserved Domains Database

More...CDDi		cd01721, Sm_D3, 1 hit

Database of protein disorder

More...DisProti		DP01707

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR027141, LSm4/Sm_D1/D3
IPR001163, LSM_dom_euk/arc
IPR010920, LSM_dom_sf
IPR034099, SmD3

The PANTHER Classification System

More...PANTHERi		PTHR23338, PTHR23338, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01423, LSM, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00651, Sm, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF50182, SSF50182, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P62323-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY 
        60         70         80         90        100
RDGRVAQLEQ VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA 
       110        120 
AILKAQVAAR GRGRGMGRGN IFQKRR
Length:126
Mass (Da):13,916
Last modified:July 5, 2004 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i59A6E78E860AA3E0
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
BC070616 mRNA Translation: AAH70616.1

NCBI Reference Sequences

More...RefSeqi		NP_001084936.1, NM_001091467.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...GeneIDi		431993

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		xla:431993

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC070616 mRNA Translation: AAH70616.1
RefSeqiNP_001084936.1, NM_001091467.1

3D structure databases

SMRiP62323
ModBaseiSearch...

Proteomic databases

MaxQBiP62323

Genome annotation databases

GeneIDi431993
KEGGixla:431993

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		431993
XenbaseiXB-GENE-1014508, snrpd3.L

Phylogenomic databases

OMAiHESLGHV
OrthoDBi1584810at2759

Family and domain databases

CDDicd01721, Sm_D3, 1 hit
DisProtiDP01707
InterProiView protein in InterPro
IPR027141, LSm4/Sm_D1/D3
IPR001163, LSM_dom_euk/arc
IPR010920, LSM_dom_sf
IPR034099, SmD3
PANTHERiPTHR23338, PTHR23338, 1 hit
PfamiView protein in Pfam
PF01423, LSM, 1 hit
SMARTiView protein in SMART
SM00651, Sm, 1 hit
SUPFAMiSSF50182, SSF50182, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSMD3_XENLA
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P62323
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: December 2, 2020
This is version 74 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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