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(-) Description

Title :  THE STRUCTURE OF THE GEMIN5 WD40 DOMAIN WITH AAUUUUUG
 
Authors :  C. Xu, H. He, Y. Li, A. Dong, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J Structural Genomics Consortium (Sgc)
Date :  17 Sep 16  (Deposition) - 26 Oct 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Snrnp Assembly, Snrna, Structural Genomics, Structural Genomics Consortium, Sgc, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Xu, H. Ishikawa, K. Izumikawa, L. Li, H. He, Y. Nobe, Y. Yamauchi, H. M. Shahjee, X. -H. Wu, Y. -T. Yu, T. Isobe, N. Takahashi, J. Min
Structural Insights Into Gemin5-Guided Selection Of Pre-Snrnas For Snrnp Assembly
Genes Dev. V. 30 2376 2016
PubMed-ID: 27881600  |  Reference-DOI: 10.1101/GAD.288340.116

(-) Compounds

Molecule 1 - GEM-ASSOCIATED PROTEIN 5
    Chains: A
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Fragment: UNP RESIDUES 1-739
    Gene: GEMIN5
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GEMIN5
 
Molecule 2 - RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*G)-3')
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U4 (118-125)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2UNX3Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:290 , SER A:293 , ASN A:294 , PRO A:342 , GLN A:350binding site for residue GOL A 803
2AC2SOFTWARETYR A:15 , SER A:113 , PHE A:155 , HOH A:982 , HOH A:1002 , HOH A:1076 , HOH B:202binding site for residue GOL A 804

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:240 -A:256

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:25 -Gly A:26
2Pro A:483 -Pro A:484
3Ile A:565 -Pro A:566

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GXH)

(-) 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    
   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:672
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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.............eeeeeeee.....eeeeeee...eeeeee.....eeeeee.....eeeeee......eeeeee....eeeee.........eeee.......eeeeee......eeeeee....eeeee.......ee........eeeeeee.........eeeeee....eeee.........eehhhhhhhhhh.......eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......hhhhh.eeeeee....eeeeehhhhhhh.....eee....eee......eeeeee......eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee.hhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gxh A   3 QEPRTLPPSPNWYCARCSDAVPGGLFGFAARTSVFLVRVGPGAGESPGTPPFRVIGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKIWDVETKTVVTEHALHQHTISTLHWSPRVKDLIVSGDEKGVVFCYWFNRNDSQHLFIEPRTIFCLTCSPHHEDLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHSIAWCPLPGEGCYLATGSKDQTIRIWSCSRGRGVMILKLPFLKRRERLWLTLHWPSNQPTQLVSSCFGGELLQWDLTQRRKYTLFSASSEGQNHSRIVFNLCPLQTEDDKQLLLSTSMDRDVKCWDIATLECSWTLPSLGGFAYSLAFSSVDIGSLAIGVGDGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPTKEGCLAFGTDDGKVGLYDTYSNKPPQISSTYHKKTVYTLAWGPPVPPMSSLALYSCGGEGIVLQHNPWKLSGEAFDINKLIRDTNSIKYKLPVHTEISWKADGKIMALGNEDGSIEIFQIPNLKLICTIQQHHKLVNTISWHHEHGSQPELSYLMASGSNNAVIYVHNLKTVIESSPESPVTITEPYRTLSGHTAKITSVAWSPHHDGRLVSASYDGTAQVWDALREEPLCNFRGHQGRLLCVAWSPLDPDCIYSGADDFCVHKWLTSMQDHSRPPQ 722
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |241       251       261       271 ||    290       300       310    || 322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482   ||  500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720  
                                                                                                                                                                                                                                        209|                               273|                             315|                                                                                                                                                                     486|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                         239                                283                              318                                                                                                                                                                      495                                                                                                                                                                                                                                   


Chain B from PDB  Type:DNA/RNA  Length:7
                                       
                 5gxh B   2 AUUUUUG   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 5GXH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:25 - Gly A:26   [ RasMol ]  
    Ile A:565 - Pro A:566   [ RasMol ]  
    Pro A:483 - Pro A:484   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GEMI5_HUMAN | Q8TEQ6: 5gxi 5h1j 5h1k 5h1l 5h1m 5h3s 5h3t 5h3u 5tee 5tef 5tha

(-) Related Entries Specified in the PDB File

5gxi RELATED ID: GEMIN5 RELATED DB: TARGETTRACK