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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GEMIN6/GEMIN7 HETERODIMER FROM THE HUMAN SMN COMPLEX
 
Authors :  Y. Ma, J. Dostie, G. Dreyfuss, G. D. Van Duyne
Date :  14 Dec 04  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sm Fold, Protein Complex, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Ma, J. Dostie, G. Dreyfuss, G. D. Van Duyne
The Gemin6-Gemin7 Heterodimer From The Survival Of Motor Neurons Complex Has An Sm Protein-Like Structure.
Structure V. 13 883 2005
PubMed-ID: 15939020  |  Reference-DOI: 10.1016/J.STR.2005.03.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GEM-ASSOCIATED PROTEIN 6
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGV67
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: GEMIN6(1-86)
    Gene: GEMIN6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GEMIN6, SIP2
 
Molecule 2 - GEM-ASSOCIATED PROTEIN 7
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24D
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: GEMIN7(47-131)
    Gene: GEMIN7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GEMIN7, SIP3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Y96)

(-) Sites  (0, 0)

(no "Site" information available for 1Y96)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y96)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y96)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y96)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3bENST000002819503bENSE00001210464chr2:39005327-3900542397GEMI6_HUMAN-00--
1.4ENST000002819504ENSE00001210471chr2:39006114-39006260147GEMI6_HUMAN1-43432A:1-43
C:1-43		43
43
1.6cENST000002819506cENSE00001290058chr2:39008659-39009598940GEMI6_HUMAN43-1671252A:43-86
C:43-86		44
44
2.1bENST000003919511bENSE00001510187chr19:45582530-45582635106GEMI7_HUMAN-00--
2.3ENST000003919513ENSE00000953130chr19:45593365-455947821418GEMI7_HUMAN1-1341342B:47-131
D:49-131		85
83

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  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:86
 aligned with GEMI6_HUMAN | Q8WXD5 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
          GEMI6_HUMAN     1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVREKLMHLF  86
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...eeeeee...eeeeeeeeee......eeeeee.....eeeeee....eeeeeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:1-43 UniProt: 1-43        ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.6c  PDB: A:43-86 UniProt: 43-167      Transcript 1 (2)
                 1y96 A   1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVREKLMHLF  86
                                    10        20        30        40        50        60        70        80      


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with GEMI7_HUMAN | Q9H840 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:85
                                    56        66        76        86        96       106       116       126     
          GEMI7_HUMAN    47 AQESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAEALLRCSDIISYTFKP 131
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeeeeeee.....eeeeeee......eeeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.3  PDB: B:47-131 UniProt: 1-134 [INCOMPLETE]                                   Transcript 2
                 1y96 B  47 AQESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAEALLRCSDIISYTFKP 131
                                    56        66        76        86        96       106       116       126     


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with GEMI6_HUMAN | Q8WXD5 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
          GEMI6_HUMAN     1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVREKLMHLF  86
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Gemin6-1y96C01 C:1-86                                                                  Pfam domains (1)
           Pfam domains (2) Gemin6-1y96C02 C:1-86                                                                  Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh....eeeeee...eeeeeeeeee......eeeeee.....eeeeee....eeeeeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: C:1-43 UniProt: 1-43        ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.6c  PDB: C:43-86 UniProt: 43-167      Transcript 1 (2)
                 1y96 C   1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVREKLMHLF  86
                                    10        20        30        40        50        60        70        80      


Chain D from PDB  Type:PROTEIN  Length:83
 aligned with GEMI7_HUMAN | Q9H840 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:83
                                    58        68        78        88        98       108       118       128   
          GEMI7_HUMAN    49 ESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAEALLRCSDIISYTFKP 131
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Gemin7-1y96D01 D:52-131                                                          Pfam domains (1)
           Pfam domains (2) ---Gemin7-1y96D02 D:52-131                                                          Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....eeeeeeeee.....eeeeeeee....eeeeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.3  PDB: D:49-131 UniProt: 1-134 [INCOMPLETE]                                 Transcript 2
                 1y96 D  49 ESLESQEQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAEALLRCSDIISYTFKP 131
                                    58        68        78        88        98       108       118       128
   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  (0, 0)

(no "SCOP Domain" information available for 1Y96)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y96)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Gemin6] (1)
(-)
Clan: no clan defined [family: Gemin7] (1)

(-) Gene Ontology  (15, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (GEMI6_HUMAN | Q8WXD5)
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:0097504    Gemini of coiled bodies    Nuclear bodies frequently found near or associated with Cajal bodies (also called coiled bodies or CBs). Gemini of coiled bodies, or 'gems', are similar in size and shape to CBs, and often indistinguishable under the microscope. Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs); they contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis, and to play a role in the etiology of spinal muscular atrophy (SMA).
    GO:0032797    SMN complex    A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
    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: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:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    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.

Chain B,D   (GEMI7_HUMAN | Q9H840)
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: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:0097504    Gemini of coiled bodies    Nuclear bodies frequently found near or associated with Cajal bodies (also called coiled bodies or CBs). Gemini of coiled bodies, or 'gems', are similar in size and shape to CBs, and often indistinguishable under the microscope. Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs); they contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis, and to play a role in the etiology of spinal muscular atrophy (SMA).
    GO:0032797    SMN complex    A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
    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: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:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    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.

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