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(-) Description

Title :  SM RNA BOUND TO GEMIN5-WD
 
Authors :  S. R. Bharath, X. Tang, H. Song
Date :  27 Oct 16  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gemin5 Smn Complex Sm Site Wd-40 Domain, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Tang, S. R. Bharath, S. Piao, V. Q. Tan, M. W. Bowler, H. Song
Structural Basis For Specific Recognition Of Pre-Snrna By Gemin5
Cell Res. V. 26 1353 2016
PubMed-ID: 27834343  |  Reference-DOI: 10.1038/CR.2016.133

(-) Compounds

Molecule 1 - GEM-ASSOCIATED PROTEIN 5
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 1-740
    Gene: GEMIN5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GEMIN5
 
Molecule 2 - RNA (5'-R(*AP*AP*UP*UP*UP*UP*UP*GP*AP*C)-3')
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (1x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:679 , HIS A:717 , SER A:718 , ARG A:719 , ARG B:679 , HIS B:717 , ARG B:719binding site for residue GOL A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H3U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:483 -Pro A:484
2Pro B:483 -Pro B:484

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H3U)

(-) Exons   (0, 0)

(no "Exon" information available for 5H3U)

(-) 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:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...........eeee...eeeeee..eeeeeee.hhhh.......eeeeeee......eeeeee........eeeeee....eeeee....eeeeee......eeeeee......eeeeee...eeeeee....eeeeee.....eeeeee......eeeeee....eeeee.....eeeeee......eeeeee......eeeeee...eeeeee....eeeeeee..............ee.......eeeee.hhh.eeeee........eee...........eeeeeeee.....eeeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.........eeee.......eeeeee......eeeeee....eeeee.......ee........eeeeeee........eeeeee....eeee.........eehhhhhhhhhh.......eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......hhhhh.eeeeee....eeeeehhhhhhhh....eee....eee......eeeeee......eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.hhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h3u A   3 QEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTPPFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVVTEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPRTIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIAWCPLPGCYLATGSKDQTIRIWSCSRGRGVMILKLPFLKRVKERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQSWRRKYTLFSASGQNHSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFAYSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPVPPMSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVHTEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHEHGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHTAKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHRGRLLCVAWSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQ 722
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     ||243       253       263       281       291       301       311       321     ||333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483 ||    502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722
                                                                                                                                                                                                                                       208|                             272|                                           327|                                                                                                                                                        485|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                        240                              281                                            330                                                                                                                                                         495                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...........eeee...eeeeee..eeeeeee.hhhh.......eeeeeeee.....eeeeee........eeeeee....eeeee....eeeeee......eeeeee......eeeeee...eeeeee....eeeeee.....eeeeee......eeeeee....eeeee.hhh..eeeee......eeeeee.....eeeeee...eeeeee.....eeeeee..........ee.......eeeee.hhh.eeeee.....eee...........eeeeeeee.....eeeeeee...eeeeee....eeeeeee.....eeeeee......eeeeee....eeeee.........eeee.......eeeeee......eeeeee....eeeee.......ee........eeeeeee........eeeeee....eeeehhhhh....eehhhhhhhhh........eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......hhhhh.eeeeee....eeeeehhhhhhhh....eee....eee......eeeeee......eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.hhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h3u B   3 QEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTPPFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVVTEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPRTIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIAWCPLPCYLATGSKDQTIRIWSCSRGRGVMILKLPFKERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQRKYTLFSASGQNHSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFAYSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPVPPMSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVHTEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHEHGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHTAKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHRGRLLCVAWSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQ 722
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202    || 244       254       264    || 286       296       306       319       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481   ||  500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720  
                                                                                                                                                                                                                                      207|                          269|                              315|     327|                                                                                                                                                        485|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                       240                           282                               319      330                                                                                                                                                         495                                                                                                                                                                                                                                   


Chain C from PDB  Type:RNA  Length:7
                                       
                 5h3u C   1 AAUUUUU   7
   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 5H3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H3U)

(-) Gene Ontology  (18, 18)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GEMI5_HUMAN | Q8TEQ6: 5gxh 5gxi 5h1j 5h1k 5h1l 5h1m 5h3s 5h3t 5tee 5tef 5tha

(-) Related Entries Specified in the PDB File

5h3s 5h3t