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(-) Description

Title :  PCID2:DSS1 STRUCTURE
 
Authors :  M. Stewart, A. M. Ellisdon
Date :  28 Jul 11  (Deposition) - 22 Feb 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pci, Mrna Nuclear Export, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Ellisdon, L. Dimitrova, E. Hurt, M. Stewart
Structural Basis For The Assembly And Nucleic Acid Binding Of The Trex-2 Transcription-Export Complex.
Nat. Struct. Mol. Biol. V. 19 328 2012
PubMed-ID: 22343721  |  Reference-DOI: 10.1038/NSMB.2235

(-) Compounds

Molecule 1 - PCI DOMAIN-CONTAINING PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 201-399
    Gene: PCID2, HT004
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CSN12-LIKE PROTEIN
 
Molecule 2 - 26S PROTEASOME COMPLEX SUBUNIT DSS1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SHFM1, DSS1, SHFDG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DELETED IN SPLIT HAND/SPLIT FOOT PROTEIN 1, SPLIT HAND/FOOT DELETED PROTEIN 1, SPLIT HAND/FOOT MALFORMATION TYPE 1 PROTEIN

 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 3T5X)

(-) Sites  (0, 0)

(no "Site" information available for 3T5X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T5X)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002485661aENSE00001039676chr7:96339203-96339000204SEM1_HUMAN1-26260--
1.4bENST000002485664bENSE00000877478chr7:96324203-9632411094SEM1_HUMAN26-57321B:38-5720
1.5bENST000002485665bENSE00001895287chr7:96318278-96317770509SEM1_HUMAN57-70141B:57-6711

(-) Sequences/Alignments

Asymmetric/Biological 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:195
 aligned with PCID2_HUMAN | Q5JVF3 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:195
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     
          PCID2_HUMAN   205 STAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC 399
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeee....eeee.......hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t5x A 205 STAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC 399
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     


Chain B from PDB  Type:PROTEIN  Length:30
 aligned with SEM1_HUMAN | P60896 from UniProtKB/Swiss-Prot  Length:70

    Alignment length:30
                                    47        57        67
           SEM1_HUMAN    38 VWEDNWDDDNVEDDFSNQLRAELEKHGYKM  67
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .eehhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4b           ---------- Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.5b   Transcript 1 (2)
                 3t5x B  38 VWEDNWDDDNVEDDFSNQLRAELEKHGYKM  67
                                    47        57        67
   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 3T5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T5X)

(-) Gene Ontology  (16, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PCID2_HUMAN | Q5JVF3)
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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:2000117    negative regulation of cysteine-type endopeptidase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of cysteine-type endopeptidase activity.
    GO:0045579    positive regulation of B cell differentiation    Any process that activates or increases the frequency, rate or extent of B cell differentiation.
    GO:0090267    positive regulation of mitotic cell cycle spindle assembly checkpoint    Any process that increases the rate, frequency, or extent of the mitotic cell cycle spindle assembly checkpoint, a cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Chain B   (SEM1_HUMAN | P60896)
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:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0043248    proteasome assembly    The aggregation, arrangement and bonding together of a mature, active proteasome complex.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0032039    integrator complex    A protein complex that stably associates with the C-terminus of RNA polymerase II and mediates 3'-end processing of small nuclear RNAs generated by RNA polymerase II.
    GO:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
    GO:0008541    proteasome regulatory particle, lid subcomplex    The subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SEM1_HUMAN | P60896: 1iyj 1miu 1mje 5gjq 5gjr 5l4k 5ln3 5m32 5t0c 5t0g 5t0h 5t0i 5t0j

(-) Related Entries Specified in the PDB File

3t5x