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(-) Description

Title :  U1-70K IN COMPLEX WITH U1 SNRNA STEM-LOOPS 1 AND U1-A RRM IN COMPLEX WITH STEM-LOOP 2
 
Authors :  C. Oubridge, Y. Kondo, A. M. Van Roon, K. Nagai
Date :  14 May 14  (Deposition) - 31 Dec 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  B,V
Keywords :  U1-70K, U1 Snrnp, Pre-Mrna Splicing, Spliceosome, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kondo, C. Oubridge, A. M. Van Roon, K. Nagai
Crystal Structure Of Human U1 Snrnp, A Small Nuclear Ribonucleoprotein Particle, Reveals The Mechanism Of 5' Splice Site Recognition.
Elife V. 4 2015
PubMed-ID: 25555158  |  Reference-DOI: 10.7554/ELIFE.04986
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - U1 SNRNA STEM-LOOPS 1 AND 2 (55-MER)
    Chains: V
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RNA IS A DUMBELL-SHAPED FUSION OF U1 SNRNA STEM-LOOP 1 AND THE APICAL PART OF U1 SNRNA STEM-LOOP 2 JOINED BY A 3 BASE PAIR LINKER. TRANSCRIBED BY T7 RNA POLYMERASE FROM A LINEARISED PLASMID TEMPLATE.
    Other Details - Source: SEE COMPOUND DETAILS.
    Synthetic: YES
 
Molecule 2 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A,U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KDA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET13
    Expression System Strain: PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SNRPA, SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1
    Mutation: YES
    Organism Common: PIG, HUMAN
    Organism Scientific: SUS SCROFA, HOMO SAPIENS
    Organism Taxid: 9823, 9606
    Other Details: BOTH THIS PROTEIN AND U1-70K ARE EXPRESSED TOGETHER AS A FUSION PROTEIN. THE C-TERMINUS OF U1-A AND THE LINKER PEPTIDE ARE DISORDERED IN THE STRUCTURE. THE TWO PROTEINS HAVE BEEN GIVEN SEPARATE CHAIN IDENTIFIERS SO THAT THEIR NORMAL NUMBERING IS PRESERVED., U1-A AND THIS PROTEIN ARE EXPRESSED TOGETHER AS A FUSION PROTEIN. THE C-TERMINUS OF U1-A AND THE LINKER PEPTIDE ARE DISORDERED IN THE STRUCTURE. THE TWO PROTEINS HAVE BEEN GIVEN SEPARATE CHAIN IDENTIFIERS SO THAT THEIR NORMAL NUMBERING IS PRESERVED.
    Synonym: U1A,SNRNP70

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2IMD1Ligand/IonIMIDAZOLE
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA V:91 , U V:92 , G V:103 , HOH V:314 , HOH V:318 , HOH V:319 , HOH V:329binding site for residue MG V 201
2AC2SOFTWAREU V:92 , HOH V:317 , HOH V:319binding site for residue MG V 202
3AC3SOFTWARELEU B:151 , TRP B:154 , HOH B:420binding site for residue MG B 301
4AC4SOFTWAREASP B:92 , C V:71 , U V:72binding site for residue IMD B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PKD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PKD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PKD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PKD)

(-) Exons   (0, 0)

(no "Exon" information available for 4PKD)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhh...eeeeee.........eeeee.hhhhhhhhhhhhh.........eeee....hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee.hhhhhhhhhhhh...ee..ee.eeee..........hhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pkd B   6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVEETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRG 267
                                    15        25        35        45        55        65        75        85        95       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267
                                                                                                                           103|                                                                                                                                             
                                                                                                                            126                                                                                                                                             


Chain V from PDB  Type:RNA  Length:55
                                                                                       
                 4pkd V  59 xGAUCCAUUGCACUCCGGAUCCAGGAGAUACCAUGAUCACGAAGGUGGUUUUCCU 113
                            |       68        78        88        98       108     
                           59-GTP
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  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 4PKD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PKD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PKD)

(-) Gene Ontology  (27, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RU17_HUMAN | P08621: 2l5i 2l5j 3cw1 3pgw 4pjo

(-) Related Entries Specified in the PDB File

1urn U1-A PROTEIN IN COMPLEX WITH STEM-LOOP 2 RNA.
3cw1 5.5 A STRUCTURE OF RECOMBINANT U1 SNRNP, WHICH CONTAINS U1-70K RRM AND HELIX 0 BOUND TO STEM-LOOP 1.
3pgw 4.4 A STRUCTURE OF NATIVE, PROTEASE-TREATED U1 SNRNP, WHICH CONTAINS U1-70K RRM AND HELIX 0 BOUND TO STEM-LOOP 1.