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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UTP22 AND RRP7 COMPLEX FROM SACCHAROMYCES CEREVISIAE
 
Authors :  J. Lin, K. Ye
Date :  08 Aug 13  (Deposition) - 06 Nov 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleolus, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lin, J. Lu, Y. Feng, M. Sun, K. Ye
An Rna-Binding Complex Involved In Ribosome Biogenesis Contains A Protein With Homology To Trna Cca-Adding Enzyme.
Plos Biol. V. 11 01669 2013
PubMed-ID: 24130456  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001669

(-) Compounds

Molecule 1 - U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 22
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: HIGH 5
    Expression System Plasmid: PFASTBAC-1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: UTP22, YGR090W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: U3 SNORNA-ASSOCIATED PROTEIN 22, U THREE PROTEIN 22
 
Molecule 2 - RIBOSOMAL RNA-PROCESSING PROTEIN 7
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: HIGH 5
    Expression System Plasmid: PFASTBAC-1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: RRP7, YCL031C, YCL184, YCL31C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1PGE3Ligand/IonTRIETHYLENE GLYCOL
2SO411Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:192 , TYR A:350 , LYS A:353 , LYS A:354 , HOH A:1763BINDING SITE FOR RESIDUE SO4 A 1301
02AC2SOFTWARESER A:376 , SER A:377 , GLY A:389 , THR A:390 , HOH A:1493 , HOH A:1930BINDING SITE FOR RESIDUE SO4 A 1302
03AC3SOFTWARESER A:384 , LEU A:385 , HOH A:1424 , HOH A:1890BINDING SITE FOR RESIDUE SO4 A 1303
04AC4SOFTWARELEU A:574 , GLY A:575 , ASP A:576 , ARG A:577 , LYS A:626 , THR A:629 , LYS A:630 , HOH A:1411BINDING SITE FOR RESIDUE SO4 A 1304
05AC5SOFTWARELYS A:166 , ARG A:597 , TYR A:600BINDING SITE FOR RESIDUE SO4 A 1305
06AC6SOFTWAREARG A:656 , PHE A:658 , LYS A:659BINDING SITE FOR RESIDUE SO4 A 1306
07AC7SOFTWAREHIS A:923 , ARG A:1063 , LEU A:1067 , PRO A:1091 , GLY A:1092 , LEU A:1093 , HOH A:1658BINDING SITE FOR RESIDUE SO4 A 1307
08AC8SOFTWAREHIS A:1194 , LYS A:1195 , ARG A:1197BINDING SITE FOR RESIDUE SO4 A 1308
09AC9SOFTWAREARG A:822 , HOH A:1556BINDING SITE FOR RESIDUE SO4 A 1309
10BC1SOFTWARELYS A:410 , HIS A:414 , ILE A:861 , ARG A:865 , HOH A:1440 , HOH A:1968BINDING SITE FOR RESIDUE SO4 A 1310
11BC2SOFTWAREARG A:92 , GLU A:96 , LYS A:423 , LYS A:427 , ASN A:500BINDING SITE FOR RESIDUE SO4 A 1311
12BC3SOFTWARETRP A:968 , ASN A:969 , LYS A:971 , THR A:1065 , LYS A:1069BINDING SITE FOR RESIDUE PGE A 1312
13BC4SOFTWARELYS A:115 , LYS A:117 , GLN A:118 , LYS A:119BINDING SITE FOR RESIDUE PGE A 1313
14BC5SOFTWARETYR A:1152 , PHE B:93 , PHE B:171BINDING SITE FOR RESIDUE PGE B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M5D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:164 -Pro A:165
2Ala A:946 -Pro A:947

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M5D)

(-) Exons   (0, 0)

(no "Exon" information available for 4M5D)

(-) 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:1098
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh............hhhhh.........eeeeehhhhh.........eeeeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh...eeeeeee.....hhhh.eeeeeeee......hhhhhh...........hhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh......eeee......eee........eee...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhh.....hhhhhh.eeeeee....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....ee.........hhhhh.....eeeeeeee........eeeeee.....hhhhhhhhhhhh..eeeee.....eeeeee.......hhhhhhhhhhhhhhh....eeehhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhh................eeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..........eeeeee.....eeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh......ee..........hhhhhhhhhhhhhhhhhhh.........ee..............hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh........eeeeee....................hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhh.....eeeeeeee.hhhh..ee........eee....eeeehhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4m5d A   81 TATESYDIHIARETAELFKSNIFKLQIDELLEQVKLKQKHVLKVEKFLHKLYDILQEIPDWEEKSLAEVDSFFKNKIVSVPFVDPKPIPQNTNYKFNYKKPDISLIGSFALKAGIYQPNGSSIDTLLTMPKELFEKKDFLNFRCLHKRSVYLAYLTHHLLILLKKDKLDSFLQLEYSYFDNDPLLPILRISCSKDYNFYKTRFSINLLIGFPYKVFEPKKLLPNRNCIRILPATPLYNFSVLSSSTHENYLKYLYKTKKQTESFVEATVLGRLWLQQRGFSSNMSHSGSLGGFGTFEFTILMAALLNGGGINSNKILLHGFSSYQLFKGVIKYLATMDLCHDGHLQFHSNPASKYIDEGFQTPTLFDKSTKVNILTKMTVSSYQILKEYAGETLRMLNNVVQDQFSNIFLTNISRFDNLKYDLCYDVQLPLGKYNNLETSLAATFGSMERVKFITLENFLAHKITNVARYALGDRIKYIQIEMVGQKSDFPITKRKVYSNTGGNHFNFDFVRVKLIVNPSECDKLVTKGPAHSETMSTEAAVFKNFWGIKSSLRRFKDGSITHCCVWSTSSSEPIISSIVNFALQKHVSKKAQISNETIKKFHNFLPLPNLPSSAKTSVLNLSSFFNLKKSFDDLYKIIFQMKLPLSVKSILPVGSAFRYTSLCQPVPFAYSDPDFFQDVILEFETSPKWPDEITSLEKAKTAFLLKIQEELSANSSTYRSFFSRDESIPYNLEIVTLNILTPEGYGFKFRVLTERDEILYLRAIANARNELKPELEATFLKFTAKYLASVRHTRTLENISHSYQFYSPVVRLFKRWLDTHLLLGHITDELAELIAIKPFVDPAPYFIPGSLENGFLKVLKFISQWNWKDDPLILDLVKPEERLTLAQYKGIQMNFTNLRNSDPNGTHLQFFVASKNDPSGILYSSGIPLPIATRLTALAKVAVNLLQTHGLNQQTINLLFTPGLKDYDFVVDLRTPIGLKSSCGILSAPSNFPENLNDLSEKMDPTYQLVKYLNLKYKNSLILSSRKYIGVNGGEKGDKNVITGLIKPLFKGAHKFRVNLDCNVKPVDDENVILNKEAIFHEIAAFGNDMVINFETD 1237
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   ||  287       297       307       317|      335       345       355       365       375       385       395       405       415       425       435       445|      462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982||    1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229        
                                                                                                                                                                                                                           274|                                317|                                                                                                                    445|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               983|                                                                                                      1116|                                                                                                             
                                                                                                                                                                                                                            282                                 326                                                                                                                     453                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               1010                                                                                                       1128                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..........eeeeeeee....hhhhh.eeeee......hhhhhhhhhhhhhhhh.....eeeee..........hhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m5d B    3 IEDISAMKNGFIVVPFKLPDHKALPASLHFMFAKRHQSSNSNESDCLFLVNLPLLSNIEHMKKFVGQLCGKYDTVSHVEELLYNDEFGLHEVDLSALTSPRNTALLKFVDAASINNCWNALKKYSNLHAKHPNELFEWTYTTPSFTTFVNFYKPLDIDYLKEDIHTHMA  189
                                    12        22    ||  36        46        56        66        76        86        96       120       130       140       150       160       170       180         
                                                   27|                                                                      105|                                                                     
                                                    32                                                                       120
   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 4M5D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M5D)

(-) Gene Ontology  (16, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ala A:946 - Pro A:947   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        RRP7_YEAST | P25368: 2mby 5wyj 5wyk
        UTP22_YEAST | P53254: 5wyj 5wyk

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