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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF AN RNA POLYMERASE RIBOZYME COMPLEXED WITH AN ANTIGEN BINDING ANTIBODY FRAGMENT
 
Authors :  Y. Koldobskaya, E. M. Duguid, D. M. Shechner, S. Koide, A. A. Kossiakoff D. P. Bartel, J. A. Piccirilli
Date :  01 Sep 09  (Deposition) - 02 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,H,L,M
Biol. Unit 1:  H,L,M  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Catalytic Rna, Protein Rna Complex, Rna Polymerase Ribozyme, Rna Hairpin Epitope, Immune System - Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Shechner, R. A. Grant, S. C. Bagby, Y. Koldobskaya, J. A. Piccirilli, D. P. Bartel
Crystal Structure Of The Catalytic Core Of An Rna-Polymeras Ribozyme.
Science V. 326 1271 2009
PubMed-ID: 19965478  |  Reference-DOI: 10.1126/SCIENCE.1174676
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB LIGHT CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MAN
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MAN
 
Molecule 3 - CLASS I LIGASE PRODUCT
    Chains: M, C
    Engineered: YES
    Other Details: SYN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHLM
Biological Unit 1 (1x):    HLM
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 37)

Asymmetric Unit (3, 37)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2CL2Ligand/IonCHLORIDE ION
3MG33Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:65 , ASP B:2 , A M:21BINDING SITE FOR RESIDUE CD B 214
02AC2SOFTWAREA C:21 , ASP H:65 , ASP L:2BINDING SITE FOR RESIDUE CD L 214
03AC3SOFTWAREASP B:186 , ASP L:186BINDING SITE FOR RESIDUE MG L 215
04AC4SOFTWAREARG A:110 , SER B:51BINDING SITE FOR RESIDUE CL B 215
05AC5SOFTWAREARG H:110 , SER L:51BINDING SITE FOR RESIDUE CL L 216
06AC6SOFTWAREHOH M:138 , HOH M:139 , HOH M:140 , HOH M:141 , HOH M:142 , HOH M:143BINDING SITE FOR RESIDUE MG M 122
07AC7SOFTWAREHOH M:144 , HOH M:145 , HOH M:146 , HOH M:147 , HOH M:148 , HOH M:149BINDING SITE FOR RESIDUE MG M 123
08AC8SOFTWAREHOH M:150 , HOH M:151 , HOH M:152 , HOH M:153 , HOH M:154 , HOH M:155BINDING SITE FOR RESIDUE MG M 124
09AC9SOFTWAREHOH M:156 , HOH M:157 , HOH M:158 , HOH M:159 , HOH M:160 , HOH M:161BINDING SITE FOR RESIDUE MG M 125
10BC1SOFTWAREHOH H:227 , HOH H:228 , HOH M:162 , HOH M:163 , HOH M:164BINDING SITE FOR RESIDUE MG M 126
11BC2SOFTWAREA M:31 , A M:32BINDING SITE FOR RESIDUE MG M 127
12BC3SOFTWAREG M:2 , HOH M:165 , HOH M:166 , HOH M:167 , HOH M:168 , HOH M:169BINDING SITE FOR RESIDUE MG M 128
13BC4SOFTWAREHOH M:170 , HOH M:171 , HOH M:172 , HOH M:173 , HOH M:174 , HOH M:175BINDING SITE FOR RESIDUE MG M 129
14BC5SOFTWAREA M:71 , G M:72 , U M:106BINDING SITE FOR RESIDUE MG M 130
15BC6SOFTWAREG M:45 , G M:46 , C M:47BINDING SITE FOR RESIDUE MG M 131
16BC7SOFTWAREHOH M:176 , HOH M:177 , HOH M:178 , HOH M:179 , HOH M:180 , HOH M:181BINDING SITE FOR RESIDUE MG M 132
17BC8SOFTWAREG M:77BINDING SITE FOR RESIDUE MG M 133
18BC9SOFTWAREHOH M:182 , HOH M:183 , HOH M:184 , HOH M:185 , HOH M:186 , HOH M:187BINDING SITE FOR RESIDUE MG M 134
19CC1SOFTWAREG M:41BINDING SITE FOR RESIDUE MG M 135
20CC2SOFTWAREA M:56 , C M:63BINDING SITE FOR RESIDUE MG M 136
21CC3SOFTWAREG M:74BINDING SITE FOR RESIDUE MG M 137
22CC4SOFTWAREHOH C:138 , HOH C:139 , HOH C:140 , HOH C:141 , HOH C:142 , HOH C:143BINDING SITE FOR RESIDUE MG C 122
23CC5SOFTWAREHOH C:144 , HOH C:145 , HOH C:146 , HOH C:147 , HOH C:148 , HOH C:149BINDING SITE FOR RESIDUE MG C 123
24CC6SOFTWAREHOH C:150 , HOH C:151 , HOH C:152 , HOH C:153 , HOH C:154 , HOH C:155BINDING SITE FOR RESIDUE MG C 124
25CC7SOFTWAREHOH C:156 , HOH C:157 , HOH C:158 , HOH C:159 , HOH C:160 , HOH C:161BINDING SITE FOR RESIDUE MG C 125
26CC8SOFTWAREHOH A:227 , HOH C:162 , HOH C:163 , HOH C:164 , HOH C:165BINDING SITE FOR RESIDUE MG C 126
27CC9SOFTWAREA C:31 , A C:32BINDING SITE FOR RESIDUE MG C 127
28DC1SOFTWAREG C:2 , HOH C:166 , HOH C:167 , HOH C:168 , HOH C:169 , HOH C:170BINDING SITE FOR RESIDUE MG C 128
29DC2SOFTWAREHOH C:171 , HOH C:172 , HOH C:173 , HOH C:174 , HOH C:175 , HOH C:176BINDING SITE FOR RESIDUE MG C 129
30DC3SOFTWAREA C:71 , G C:72 , U C:106BINDING SITE FOR RESIDUE MG C 130
31DC4SOFTWAREG C:45 , G C:46 , C C:47BINDING SITE FOR RESIDUE MG C 131
32DC5SOFTWAREHOH C:177 , HOH C:178 , HOH C:179 , HOH C:180 , HOH C:181 , HOH C:182BINDING SITE FOR RESIDUE MG C 132
33DC6SOFTWAREG C:77BINDING SITE FOR RESIDUE MG C 133
34DC7SOFTWAREHOH C:183 , HOH C:184 , HOH C:185 , HOH C:186 , HOH C:187 , HOH C:188BINDING SITE FOR RESIDUE MG C 134
35DC8SOFTWAREG C:41BINDING SITE FOR RESIDUE MG C 135
36DC9SOFTWAREA C:56 , C C:63BINDING SITE FOR RESIDUE MG C 136
37EC1SOFTWAREG C:74BINDING SITE FOR RESIDUE MG C 137

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:25 -A:99
2A:152 -A:208
3B:24 -B:89
4B:135 -B:195
5H:25 -H:99
6H:152 -H:208
7L:24 -L:89
8L:135 -L:195

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser L:8 -Pro L:9
2Phe L:95 -Pro L:96
3Tyr L:141 -Pro L:142
4Phe H:158 -Pro H:159
5Glu H:160 -Pro H:161
6Ser B:8 -Pro B:9
7Phe B:95 -Pro B:96
8Tyr B:141 -Pro B:142
9Phe A:158 -Pro A:159
10Glu A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IVK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IVK)

(-) Exons   (0, 0)

(no "Exon" information available for 3IVK)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ivkA01 A:3-125 Immunoglobulins                                                                                            3ivkA02 A:126-225 Immunoglobulins                                                                   - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeeee..hhhhheeeeeeee.hhhhhh..eeee...eee..........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ivk A   3 SEVQLVESGGGLVQPGGSLRLSCAASGFYISYSSIHWVRQAPGKGLEWVASISPYSGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARQGYRRRSGRGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3ivkb1 B:1-108 automated matches                                                                           d3ivkb2 B:109-213 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------3ivkB02 B:110-213 Immunoglobulins                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ivk B   1 SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSFPSTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain C from PDB  Type:RNA  Length:128
                                                                                                                                                                
                 3ivk C  -7 UCCAGUAGGAACACUAUACUACUGGAUAAUCAAAGACAAAUCUGCCCGAAGGGCUUGAGAACAUCGAAACACGAUGCAGAGGUGGCAGCCUCCGGUGGGUUAAAACCCAACGUUCUCAACAAUAGUGA 121
                                  || 3        13        23        33        43        53        63        73        83        93       103       113        
                                 -1|                                                                                                                        
                                   1                                                                                                                        


Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ivkH01 H:3-125 Immunoglobulins                                                                                            3ivkH02 H:126-225 Immunoglobulins                                                                   - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeeee..hhhhheeeeeeee.hhhhhh..eeee...eee..........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ivk H   3 SEVQLVESGGGLVQPGGSLRLSCAASGFYISYSSIHWVRQAPGKGLEWVASISPYSGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARQGYRRRSGRGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3ivkl1 L:1-108 automated matches                                                                           d3ivkl2 L:109-213 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------3ivkL02 L:110-213 Immunoglobulins                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ivk L   1 SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSFPSTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain M from PDB  Type:RNA  Length:128
                                                                                                                                                                
                 3ivk M  -7 UCCAGUAGGAACACUAUACUACUGGAUAAUCAAAGACAAAUCUGCCCGAAGGGCUUGAGAACAUCGAAACACGAUGCAGAGGUGGCAGCCUCCGGUGGGUUAAAACCCAACGUUCUCAACAAUAGUGA 121
                                  || 3        13        23        33        43        53        63        73        83        93       103       113        
                                 -1|                                                                                                                        
                                   1
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  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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IVK)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3IVK)

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