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(-) Description

Title :  CRYSTAL STRUCTURE OF WD40 REPEAT DOMAINS OF GEMIN5 IN COMPLEX WITH 13-NT U4 SNRNA FRAGMENT
 
Authors :  Y. Wang, W. Jin, C. P. Liu, N. Yang, M. Jin, Y. Cong, M. Wang, R. M. Xu
Date :  10 Oct 16  (Deposition) - 23 Nov 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Wd Repeat, Gemin5, Smn, Rna Binding, U4 Snrna, Splicing-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Jin, Y. Wang, C. P. Liu, N. Yang, M. Jin, Y. Cong, M. Wang, R. M. Xu
Structural Basis For Snrna Recognition By The Double-Wd40 Repeat Domain Of Gemin5
Genes Dev. V. 30 2391 2016
PubMed-ID: 27881601  |  Reference-DOI: 10.1101/GAD.291377.116

(-) Compounds

Molecule 1 - GEM-ASSOCIATED PROTEIN 5
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell: SF21
    Expression System Plasmid: PFASTBAC-HTC
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 1-726
    Gene: GEMIN5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GEMIN5
 
Molecule 2 - U4 SNRNA (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 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 5H1K)

(-) Sites  (0, 0)

(no "Site" information available for 5H1K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H1K)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:25 -Gly A:26
2Pro A:483 -Pro A:484
3Ile A:565 -Pro A:566
4Gly B:25 -Gly B:26
5Pro B:483 -Pro B:484
6Ile B:565 -Pro B:566

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H1K)

(-) Exons   (0, 0)

(no "Exon" information available for 5H1K)

(-) 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:674
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               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.hhh..eeeee......eeeeee.............eeeeee...eeeeee....eeeeeee..........ee.......eeeee.hhh.eeeee....eee.hhhhhhhh....eeeeeeee.....eeeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.........eeee.......eeeeee......eeeeee....eeeee.......ee........eeeeeee...........eeeeee....eeee.........eehhhhhhhhhh.......eeeeee.....eeeeee...eeeeee....eeeeeee.....eeeeee......hhhhh.eeeeee....eeeeehhhhhhhh....eee....eee......eeeeee......eeeeee....eeeee.hhheeeeee......eeeeee......eeeeee....eeeee.hhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h1k A   3 QEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTPPFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVVTEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPRTIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIAWCPLPGEDCLSIGCYLATGSKDQTIRIWSCSRGRGVMILKLPFKERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQKYTLFSASSEGQNHSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFAYSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPVPPMSLPSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVHTEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHEHGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHTAKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHRGRLLCVAWSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQ 722
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 ||    246       256       266  ||   288       298       308      |322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    || 498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718    
                                                                                                                                                                                                                                             214|                           269|                              315|                                                                                                                                                                    487|                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                              239                            282                               320                                                                                                                                                                     494                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:690
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               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....hhhhh....eeeeeeee.....eeeeeee....eeeee.....eeeee......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
                 5h1k B  -7 GAMGIRNSMGQEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTPPFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVVTEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPRTIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIAWCPLPGEDCLSIGCYLATGSKDQTIRIWSCSRGRGVMILKLPFLKERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQSWRRKYTLFSASSEGQNHSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFAYSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPVPPMSLPSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVHTEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHEHGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHTAKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHRGRLLCVAWSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQG 723
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 ||    246       256       266   ||  287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487|      503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723
                                                                                                                                                                                                                                                       214|                            270|                                                                                                                                                                                                          487|                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                        239                             282                                                                                                                                                                                                           494                                                                                                                                                                                                                                     


Chain C from PDB  Type:RNA  Length:13
                                             
                 5h1k C  -2 GCAAUUUUUGACA  10
                                     7   


Chain D from PDB  Type:RNA  Length:12
                                            
                 5h1k D  -1 CAAUUUUUGACA  10
                                     8
   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 5H1K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H1K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H1K)

(-) Gene Ontology  (18, 18)

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  Cis Peptide Bonds
    Gly A:25 - Gly A:26   [ RasMol ]  
    Gly B:25 - Gly B:26   [ RasMol ]  
    Ile A:565 - Pro A:566   [ RasMol ]  
    Ile B:565 - Pro B:566   [ RasMol ]  
    Pro A:483 - Pro A:484   [ RasMol ]  
    Pro B:483 - Pro B:484   [ RasMol ]  
 
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  5h1k
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 Related Entries

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

UniProtKB/Swiss-Prot
        GEMI5_HUMAN | Q8TEQ6: 5gxh 5gxi 5h1j 5h1l 5h1m 5h3s 5h3t 5h3u 5tee 5tef 5tha

(-) Related Entries Specified in the PDB File

5h1j 5h1l 5h1m