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(-) Description

Title :  U1A MUTANT/RNA COMPLEX + GLYCEROL
 
Authors :  C. Oubridge, N. Ito, P. R. Evans, C. -H. Teo, K. Nagai
Date :  04 Jan 95  (Deposition) - 08 Mar 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,P,Q,R
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Biol. Unit 3:  C,R  (1x)
Keywords :  Protein-Rna Complex, Single Strand, Overhanging Base, Hairpin Loop, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Oubridge, N. Ito, P. R. Evans, C. H. Teo, K. Nagai
Crystal Structure At 1. 92 A Resolution Of The Rna-Binding Domain Of The U1A Spliceosomal Protein Complexed With An Rn Hairpin.
Nature V. 372 432 1994
PubMed-ID: 7984237  |  Reference-DOI: 10.1038/372432A0

(-) Compounds

Molecule 1 - RNA (5'- R(*AP*AP*UP*CP*CP*AP*UP*UP*GP*CP*AP*CP*UP*CP*CP*GP*G P*AP*UP*UP*U)- 3')
    ChainsP, Q, R
    EngineeredYES
    SyntheticYES
 
Molecule 2 - PROTEIN (U1A)
    Cell LineFETAL BRAIN CDNA LIBRARY
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System GeneU1A (2-98, Y31H, Q36R)
    Expression System PlasmidPKN172
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCPQR
Biological Unit 1 (1x)A  P  
Biological Unit 2 (1x) B  Q 
Biological Unit 3 (1x)  C  R

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , ARG B:70 , TYR B:86BINDING SITE FOR RESIDUE CL B 1
2AC2SOFTWAREALA A:2 , VAL A:3 , PHE C:77 , TYR C:78 , HOH C:4008 , HOH C:4063BINDING SITE FOR RESIDUE GOL C 2000
3AC3SOFTWAREARG B:36 , HOH B:5007 , PHE C:37 , GLU C:61 , SER C:64 , HOH C:4026 , HOH C:4060BINDING SITE FOR RESIDUE GOL B 3000
4AC4SOFTWAREPRO B:76 , ASN C:15 , ASN C:16 , ARG C:83 , HOH C:4006 , HOH C:4012 , HOH C:4017 , U R:8 , HOH R:101 , HOH R:107BINDING SITE FOR RESIDUE GOL C 4000
5AC5SOFTWAREPHE B:77 , TYR B:78 , GLU C:5 , HOH C:4075BINDING SITE FOR RESIDUE GOL B 5000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
 
208-282
  3A:10-89
B:10-89
C:10-89
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
 
208-282
  1A:10-89
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
 
208-282
  1-
B:10-89
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
 
208-282
  1-
-
C:10-89
-

(-) Exons   (3, 9)

Asymmetric Unit (3, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002435631ENSE00001052136chr19:41256779-41257386608SNRPA_HUMAN1-25253A:2-25
B:2-25
C:2-25
24
24
24
1.2ENST000002435632ENSE00000707951chr19:41263237-41263409173SNRPA_HUMAN25-82583A:25-82
B:25-82
C:25-82
58
58
58
1.3ENST000002435633ENSE00000707956chr19:41265336-41265515180SNRPA_HUMAN83-142603A:83-97
B:83-97
C:83-97
15
15
15
1.4ENST000002435634ENSE00000707961chr19:41268806-41268979174SNRPA_HUMAN143-200580--
1.5ENST000002435635ENSE00000842333chr19:41269492-4126958089SNRPA_HUMAN201-230300--
1.6ENST000002435636ENSE00000842334chr19:41270913-41271290378SNRPA_HUMAN230-282530--

(-) 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:96
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
           SNRPA_HUMAN    2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
               SCOP domains d1urna_ A: Splicesomal U1A protein                                                               SCOP domains
               CATH domains 1urnA00 A:2-97  [code=3.30.70.330, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee.......hhhhhhhhhhhhhhh..eeeeee.........eeeee..hhhhhhhhhhh..........eeee.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------RRM  PDB: A:10-89 UniProt: 10-89                                                -------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:2-25   ---------------------------------------------------------Exon 1.3        Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: A:25-82 UniProt: 25-82                     --------------- Transcript 1 (2)
                  1urn A  2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
                                    11        21        31        41        51        61        71        81        91      

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
           SNRPA_HUMAN    2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
               SCOP domains d1urnb_ B: Splicesomal U1A protein                                                               SCOP domains
               CATH domains 1urnB00 B:2-97  [code=3.30.70.330, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee.......hhhhhhhhhhhhhhh..eeeeee.........eeeee..hhhhhhhhhhh..........eeee.....hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------RRM  PDB: B:10-89 UniProt: 10-89                                                -------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:2-25   ---------------------------------------------------------Exon 1.3        Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: B:25-82 UniProt: 25-82                     --------------- Transcript 1 (2)
                  1urn B  2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
                                    11        21        31        41        51        61        71        81        91      

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
           SNRPA_HUMAN    2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
               SCOP domains d1urnc_ C: Splicesomal U1A protein                                                               SCOP domains
               CATH domains 1urnC00 C:2-97  [code=3.30.70.330, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee.......hhhhhhhhhhhhhhh..eeeeee.........eeeee..hhhhhhhhhhh..........eeee.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------RRM  PDB: C:10-89 UniProt: 10-89                                                -------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:2-25   ---------------------------------------------------------Exon 1.3        Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: C:25-82 UniProt: 25-82                     --------------- Transcript 1 (2)
                  1urn C  2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
                                    11        21        31        41        51        61        71        81        91      

Chain P from PDB  Type:DNA/RNA  Length:20
                                                   
                  1urn P  1 AAUCCAUUGCACUCGGAUUU 21
                                    10  ||    21
                                       13|      
                                        15      

Chain Q from PDB  Type:RNA  Length:21
                                                    
                  1urn Q  1 AAUCCAUUGCACUCCGGAUUU 21
                                    10        20 

Chain R from PDB  Type:DNA/RNA  Length:20
                                                   
                  1urn R  1 AAUCCAUUGCACUCGGAUUU 21
                                    10  ||    21
                                       13|      
                                        15      

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SNRPA_HUMAN | P09012)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030619    U1 snRNA binding    Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA).
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0017069    snRNA binding    Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
    GO:0035614    snRNA stem-loop binding    Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
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.
cellular component
    GO:0005685    U1 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U1.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        SNRPA_HUMAN | P090121aud 1drz 1dz5 1fht 1m5k 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2a3j 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4prf 4w90 4w92 4yb1 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1URN)