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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SPLICEOSOMAL 15.5KD PROTEIN BOUND TO A U4 SNRNA FRAGMENT
 
Authors :  I. Vidovic, S. Nottrott, K. Harthmuth, R. Luhrmann, R. Ficner
Date :  29 Aug 00  (Deposition) - 19 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Rna-Binding Protein, Splicing, Rna Recognition Motif, U4 Snrna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Vidovic, S. Nottrott, K. Hartmuth, R. Luhrmann, R. Ficner
Crystal Structure Of The Spliceosomal 15. 5Kd Protein Bound To A U4 Snrna Fragment
Mol. Cell V. 6 1331 2000
PubMed-ID: 11163207  |  Reference-DOI: 10.1016/S1097-2765(00)00131-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 15.5 KD RNA BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NHP2/RS6 FAMILY PROTEIN YEL026W HOMOLOG, HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG, OTK27
 
Molecule 2 - RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')
    Chains: C, D
    Fragment: 26-47
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U4 SNRNA
    Synthetic: HUMAN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1E7K)

(-) Sites  (0, 0)

(no "Site" information available for 1E7K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E7K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:11 -Pro A:12
2Glu A:61 -Pro A:62
3Tyr B:11 -Pro B:12
4Glu B:61 -Pro B:62

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034155T19NNH2L1_HUMANPolymorphism1802521A/BT19N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034155T19NNH2L1_HUMANPolymorphism1802521AT19N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034155T19NNH2L1_HUMANPolymorphism1802521BT19N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L7AEPS01082 Ribosomal protein L7Ae signature.NH2L1_HUMAN73-90
 		  2A:73-90
B:73-90
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L7AEPS01082 Ribosomal protein L7Ae signature.NH2L1_HUMAN73-90
 		  1A:73-90
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L7AEPS01082 Ribosomal protein L7Ae signature.NH2L1_HUMAN73-90
 		  1-
B:73-90

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003552572aENSE00001488410chr22:42084913-42084798116NH2L1_HUMAN1-110--
1.6bENST000003552576bENSE00000656116chr22:42076368-42076248121NH2L1_HUMAN2-42412A:4-42
B:6-42		39
37
1.7eENST000003552577eENSE00001948112chr22:42071199-420699341266NH2L1_HUMAN42-128872A:42-128
B:42-128		87
87

(-) 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:125
 aligned with NH2L1_HUMAN | P55769 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:125
                                    13        23        33        43        53        63        73        83        93       103       113       123     
          NH2L1_HUMAN     4 ADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
               SCOP domains d1e7ka_ A: Spliceosomal 15.5kd protein                                                                                        SCOP domains
               CATH domains 1e7kA00 A:4-128  [code=3.30.1330.30, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh..eeeeeee....hhhhh.hhhhhhhhhh.eeeee.hhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------N------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------RIBOSOMAL_L7AE    -------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:4-42 UniProt: 2-42   -------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.7e  PDB: A:42-128 UniProt: 42-128                                                Transcript 1 (2)
                 1e7k A   4 ADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
                                    13        23        33        43        53        63        73        83        93       103       113       123     


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with NH2L1_HUMAN | P55769 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:123
                                    15        25        35        45        55        65        75        85        95       105       115       125   
          NH2L1_HUMAN     6 VNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
               SCOP domains d1e7kb_ B: Spliceosomal 15.5kd protein                                                                                      SCOP domains
               CATH domains 1e7kB00 B:6-128  [code=3.30.1330.30, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh..eeeeeee....hhhhh.hhhhhhhhhh..eeee.hhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------N------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------RIBOSOMAL_L7AE    -------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: B:6-42 UniProt: 2-42 -------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.7e  PDB: B:42-128 UniProt: 42-128                                                Transcript 1 (2)
                 1e7k B   6 VNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
                                    15        25        35        45        55        65        75        85        95       105       115       125   


Chain C from PDB  Type:RNA  Length:17
                                                 
                 1e7k C  26 GCCAAUGAGGCCGAGGC  47
                                    35|      
                                    35|      
                                     41      


Chain D from PDB  Type:RNA  Length:17
                                                 
                 1e7k D  26 GCCAAUGAGGCCGAGGC  47
                                    35|      
                                    35|      
                                     41
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E7K)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NH2L1_HUMAN | P55769)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0034511    U3 snoRNA binding    Interacting selectively and non-covalently with U3 small nucleolar RNA.
    GO:0030621    U4 snRNA binding    Interacting selectively and non-covalently with the U4 small nuclear RNA (U4 snRNA).
    GO:0030622    U4atac snRNA binding    Interacting selectively and non-covalently with the U4atac small nuclear RNA (U4atac snRNA).
    GO:0034512    box C/D snoRNA binding    Interacting selectively and non-covalently with box C/D small nucleolar RNA.
    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).
    GO:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
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:0000470    maturation of LSU-rRNA    Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
    GO:0030490    maturation of SSU-rRNA    Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    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:0031428    box C/D snoRNP complex    A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0001651    dense fibrillar component    A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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: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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0032040    small-subunit processome    A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
    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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        NH2L1_HUMAN | P55769: 2jnb 2ozb 3jcr 3siu 3siv

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