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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN
 
Authors :  S. Walke, R. J. Young, C. Kambach, J. M. Avis, E. De La Fortelle, J. Li, K
Date :  17 Dec 98  (Deposition) - 13 Jan 00  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Snrnp, Splicing, Spliceosome, Sm, Core Snrnp Domain, Systemic Lupus Erythematosus, Sle, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Kambach, S. Walke, R. Young, J. M. Avis, E. De La Fortelle, V. A. Raker, R. Luhrmann, J. Li, K. Nagai
Crystal Structures Of Two Sm Protein Complexes And Their Implications For The Assembly Of The Spliceosomal Snrnps.
Cell(Cambridge, Mass. ) V. 96 375 1999
PubMed-ID: 10025403  |  Reference-DOI: 10.1016/S0092-8674(00)80550-4

(-) Compounds

Molecule 1 - PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)
    Chains: A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2)
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1B34)

(-) Sites  (0, 0)

(no "Site" information available for 1B34)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B34)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B34)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B34)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003004131ENSE00001137497chr18:19192260-19192404145SMD1_HUMAN1-551A:2-54
1.2ENST000003004132ENSE00001109516chr18:19202686-1920276277SMD1_HUMAN5-31271A:5-3127
1.3ENST000003004133ENSE00001109513chr18:19203709-19203900192SMD1_HUMAN31-95651A:31-8151
1.4ENST000003004134ENSE00001109508chr18:19209023-192102041182SMD1_HUMAN95-119250--
2.1ENST000003426691ENSE00002150353chr19:46195442-46195145298SMD2_HUMAN1-110--
2.3aENST000003426693aENSE00001371016chr19:46191824-46191645180SMD2_HUMAN1-61611B:26-6136
2.4ENST000003426694ENSE00000858249chr19:46190985-46190719267SMD2_HUMAN61-118581B:61-118 (gaps)58

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:80
 aligned with SMD1_HUMAN | P62314 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:80
                                    11        21        31        41        51        61        71        81
           SMD1_HUMAN     2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV  81
               SCOP domains d1b34a_ A: D1 core SNRNP protein                                                 SCOP domains
               CATH domains 1b34A00 A:2-81  [code=2.30.30.100, no name defined]                              CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....eeeeee....eeeeeeeee.....eeee.eeee......eee.eeee.hhheeeee......hhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1 -------------------------Exon 1.3  PDB: A:31-81 UniProt: 31-95 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:5-31      -------------------------------------------------- Transcript 1 (2)
                 1b34 A   2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV  81
                                    11        21        31        41        51        61        71        81


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with SMD2_HUMAN | P62316 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:93
                                    35        45        55        65        75        85        95       105       115   
           SMD2_HUMAN    26 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK 118
               SCOP domains d1b34b_ B: D2 core SNRNP protein                                                              SCOP domains
               CATH domains 1b34B00 B:26-118  [code=2.30.30.100, no name def                   ined]                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeeee....eeeeeeeee.....eeee.eeee-------------------.eee.eeee.hhheeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.3a  PDB: B:26-61 [INCOMPLETE]--------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) -----------------------------------Exon 2.4  PDB: B:61-118 (gaps) UniProt: 61-118             Transcript 2 (2)
                 1b34 B  26 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM-------------------DRYISKMFLRGDSVIVVLRNPLIAGK 118
                                    35        45        55        65       | -         -       |95       105       115   
                                                                          73                  93
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B34)

(-) Gene Ontology  (34, 58)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMD1_HUMAN | P62314)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0051170    nuclear import    The directed movement of substances into the nucleus.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0000245    spliceosomal complex assembly    The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
    GO:0000387    spliceosomal snRNP assembly    The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0034719    SMN-Sm protein complex    A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm.
    GO:0005685    U1 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U1.
    GO:0005689    U12-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
    GO:0005686    U2 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U2.
    GO:0005687    U4 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U4.
    GO:0005682    U5 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U5.
    GO:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    GO:0000243    commitment complex    A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0034709    methylosome    A large (20 S) protein complex that possesses protein arginine methyltransferase activity and modifies specific arginines to dimethylarginines in the arginine- and glycine-rich domains of several spliceosomal Sm proteins, thereby targeting these proteins to the survival of motor neurons (SMN) complex for assembly into small nuclear ribonucleoprotein (snRNP) core particles. Proteins found in the methylosome include the methyltransferase JBP1 (PRMT5), pICln (CLNS1A), MEP50 (WDR77), and unmethylated forms of SM proteins that have RG domains.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0034715    pICln-Sm protein complex    A protein complex that contains pICln (CLNS1A) and several Sm proteins, including SmD1, SmD2, SmE, SmF, and SmG.
    GO:0071011    precatalytic spliceosome    A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.
    GO:0071010    prespliceosome    A spliceosomal complex that is formed by association of the 5' splice site and the branch point sequence with specific snRNPs. The prespliceosome includes many proteins in addition to those found in the bound snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation. Prespliceosome complexes are not active for splicing, but are instead an early step in the assembly of a spliceosomal complex.
    GO:0030532    small nuclear ribonucleoprotein complex    A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.
    GO:0097526    spliceosomal tri-snRNP complex    A spliceosomal snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins.

Chain B   (SMD2_HUMAN | P62316)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0051170    nuclear import    The directed movement of substances into the nucleus.
    GO:0000245    spliceosomal complex assembly    The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
    GO:0000387    spliceosomal snRNP assembly    The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
cellular component
    GO:0034719    SMN-Sm protein complex    A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm.
    GO:0005685    U1 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U1.
    GO:0005689    U12-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
    GO:0005686    U2 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U2.
    GO:0005687    U4 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U4.
    GO:0046540    U4/U6 x U5 tri-snRNP complex    A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
    GO:0005682    U5 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U5.
    GO:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0034709    methylosome    A large (20 S) protein complex that possesses protein arginine methyltransferase activity and modifies specific arginines to dimethylarginines in the arginine- and glycine-rich domains of several spliceosomal Sm proteins, thereby targeting these proteins to the survival of motor neurons (SMN) complex for assembly into small nuclear ribonucleoprotein (snRNP) core particles. Proteins found in the methylosome include the methyltransferase JBP1 (PRMT5), pICln (CLNS1A), MEP50 (WDR77), and unmethylated forms of SM proteins that have RG domains.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0034715    pICln-Sm protein complex    A protein complex that contains pICln (CLNS1A) and several Sm proteins, including SmD1, SmD2, SmE, SmF, and SmG.
    GO:0071011    precatalytic spliceosome    A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.
    GO:0030532    small nuclear ribonucleoprotein complex    A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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  1b34
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SMD1_HUMAN | P62314: 3cw1 3jcr 3pgw 3s6n 4f7u 4pjo 4v98 4wzj 5mqf
        SMD2_HUMAN | P62316: 3cw1 3jcr 3pgw 3s6n 4f7u 4pjo 4v98 4wzj 5mqf

(-) Related Entries Specified in the PDB File

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