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(-) Description

Title :  STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON IN THE PRESENCE OF K+, MG2+ AND A HYDROLYZED OLIGONUCLEOTIDE FRAGMENT
 
Authors :  M. Marcia, A. M. Pyle
Date :  22 May 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribozyme, Self-Splicing, Retrotransposition, Spliceosome, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Marcia, A. M. Pyle
Visualizing Group Ii Intron Catalysis Through The Stages Of Splicing.
Cell(Cambridge, Mass. ) V. 151 497 2012
PubMed-ID: 23101623  |  Reference-DOI: 10.1016/J.CELL.2012.09.033

(-) Compounds

Molecule 1 - GROUP IIC INTRON
    Chains: A
    Engineered: YES
    Fragment: DOMAINS 1-5
    Organism Scientific: OCEANOBACILLUS IHEYENSIS
    Organism Taxid: 182710
    Other Details: IN VITRO TRANSCRIPTION
    Synthetic: YES
 
Molecule 2 - 5'-R(*A*UP*UP*UP*AP*UP*UP*A)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 56)

Asymmetric/Biological Unit (4, 56)
No.NameCountTypeFull Name
1EPE4Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2K19Ligand/IonPOTASSIUM ION
3MG32Ligand/IonMAGNESIUM ION
4SPM1Ligand/IonSPERMINE

(-) Sites  (51, 51)

Asymmetric Unit (51, 51)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU A:375 , C A:377 , MG A:404 , HOH A:514 , U B:5 , HOH B:101BINDING SITE FOR RESIDUE MG A 402
02AC2SOFTWAREU A:26 , U A:65BINDING SITE FOR RESIDUE MG A 403
03AC3SOFTWAREC A:358 , G A:359 , C A:377 , MG A:402 , HOH A:515 , HOH B:101BINDING SITE FOR RESIDUE MG A 404
04AC4SOFTWAREC A:145BINDING SITE FOR RESIDUE MG A 405
05AC5SOFTWAREG A:3 , U A:4 , HOH A:506BINDING SITE FOR RESIDUE MG A 406
06AC6SOFTWAREC A:360 , G A:374BINDING SITE FOR RESIDUE MG A 407
07AC7SOFTWAREG A:325BINDING SITE FOR RESIDUE MG A 408
08AC8SOFTWAREG A:107BINDING SITE FOR RESIDUE MG A 410
09AC9SOFTWAREC A:372BINDING SITE FOR RESIDUE MG A 411
10BC1SOFTWAREC A:119 , A A:174 , U A:238 , G A:239BINDING SITE FOR RESIDUE MG A 413
11BC2SOFTWAREA A:186BINDING SITE FOR RESIDUE MG A 414
12BC3SOFTWAREA A:77 , A A:105BINDING SITE FOR RESIDUE MG A 415
13BC4SOFTWAREG A:136BINDING SITE FOR RESIDUE MG A 416
14BC5SOFTWAREU A:66 , A A:67BINDING SITE FOR RESIDUE MG A 417
15BC6SOFTWAREG A:284BINDING SITE FOR RESIDUE MG A 418
16BC7SOFTWAREC A:6BINDING SITE FOR RESIDUE MG A 419
17BC8SOFTWAREG A:169BINDING SITE FOR RESIDUE MG A 420
18BC9SOFTWAREA A:184BINDING SITE FOR RESIDUE MG A 421
19CC1SOFTWAREA A:67 , G A:68BINDING SITE FOR RESIDUE MG A 422
20CC2SOFTWAREA A:154 , G A:155 , HOH A:501BINDING SITE FOR RESIDUE MG A 423
21CC3SOFTWAREU A:285BINDING SITE FOR RESIDUE MG A 424
22CC4SOFTWAREG A:382BINDING SITE FOR RESIDUE MG A 425
23CC5SOFTWAREA A:283BINDING SITE FOR RESIDUE MG A 426
24CC6SOFTWAREG A:142BINDING SITE FOR RESIDUE MG A 427
25CC7SOFTWAREA A:120 , A A:121BINDING SITE FOR RESIDUE MG A 428
26CC8SOFTWAREA A:181 , A A:223BINDING SITE FOR RESIDUE MG A 429
27CC9SOFTWAREHOH A:511BINDING SITE FOR RESIDUE MG A 430
28DC1SOFTWAREC A:286 , A A:287BINDING SITE FOR RESIDUE MG A 431
29DC2SOFTWAREA A:290 , A A:355 , A A:356BINDING SITE FOR RESIDUE MG A 432
30DC3SOFTWAREG A:14 , G A:15BINDING SITE FOR RESIDUE K A 433
31DC4SOFTWAREG A:269BINDING SITE FOR RESIDUE K A 434
32DC5SOFTWAREU A:273 , G A:275 , K A:439BINDING SITE FOR RESIDUE K A 435
33DC6SOFTWAREG A:28BINDING SITE FOR RESIDUE K A 436
34DC7SOFTWAREU A:4 , G A:107 , U A:375 , A A:376BINDING SITE FOR RESIDUE K A 437
35DC8SOFTWAREG A:264BINDING SITE FOR RESIDUE K A 438
36DC9SOFTWAREG A:275 , K A:435BINDING SITE FOR RESIDUE K A 439
37EC1SOFTWAREC A:86 , G A:87 , A A:95 , U A:96 , G A:97BINDING SITE FOR RESIDUE K A 440
38EC2SOFTWAREG A:3 , U A:4 , G A:5 , A A:376BINDING SITE FOR RESIDUE K A 441
39EC3SOFTWAREG A:32 , A A:33 , G A:34 , A A:50BINDING SITE FOR RESIDUE K A 442
40EC4SOFTWAREG A:288 , C A:358 , G A:359 , C A:377BINDING SITE FOR RESIDUE K A 443
41EC5SOFTWAREG A:92BINDING SITE FOR RESIDUE K A 445
42EC6SOFTWAREG A:194BINDING SITE FOR RESIDUE K A 446
43EC7SOFTWAREG A:266 , G A:267 , HOH A:510BINDING SITE FOR RESIDUE K A 447
44EC8SOFTWAREG A:79 , G A:80BINDING SITE FOR RESIDUE K A 449
45EC9SOFTWAREA A:297 , G A:320BINDING SITE FOR RESIDUE K A 450
46FC1SOFTWAREA A:333 , G A:335 , G A:336BINDING SITE FOR RESIDUE K A 451
47FC2SOFTWAREU A:47 , A A:49 , G A:55 , A A:56 , G A:58BINDING SITE FOR RESIDUE SPM A 452
48FC3SOFTWAREC A:39 , G A:242 , G A:243 , G A:244BINDING SITE FOR RESIDUE EPE A 453
49FC4SOFTWAREU A:96 , G A:97 , G A:98BINDING SITE FOR RESIDUE EPE A 454
50FC5SOFTWAREA A:115 , C A:116 , G A:117BINDING SITE FOR RESIDUE EPE A 455
51FC6SOFTWAREA A:77 , G A:104BINDING SITE FOR RESIDUE EPE A 456

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FAW)

(-) 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)
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Chain A from PDB  Type:RNA  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
                 4faw A   2 UGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGCCGUAUACCGAACGGUACGUACGGUGGUGUGG 391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391


Chain B from PDB  Type:RNA  Length:5
                                     
                 4faw B   1 UUUAU   5
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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 4FAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

4e8k 4e8m 4e8n 4e8p 4e8q 4e8r 4e8t 4e8v 4faq 4far 4fau 4fax 4fb0