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(-) Description

Title :  CRYSTAL STRUCTURE OF A HAIRPIN RIBOZYME IN THE CATALYTICALLY-ACTIVE CONFORMATION
 
Authors :  P. B. Rupert, A. R. Ferre-D'Amare
Date :  09 Jul 02  (Deposition) - 02 Aug 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Hairpin Ribozyme, Catalytic Rna, U1A Rna Binding Protein Docked Conformation, Substrate Inhibitor Strand, Translation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. B. Rupert, A. P. Massey, S. T. Sigurdsson, A. R. Ferre-D'Amare
Transition State Stabilization By A Catalytic Rna
Science V. 298 1421 2002
PubMed-ID: 11298439  |  Reference-DOI: 10.1126/SCIENCE.1076093
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA INHIBITOR SUBSTRATE
    ChainsA, D
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS
    SyntheticYES
 
Molecule 2 - RNA HAIRPIN RIBOZYME
    ChainsB, E
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS
    SyntheticYES
 
Molecule 3 - PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
    ChainsC, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentU1A RNA BINDING DOMAIN
    GeneSNRPA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymU1 SNRNP A PROTEIN;
U1 SNRNP-SPECIFIC PROTEIN A

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)   DEF
Biological Unit 2 (1x)ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 41)

Asymmetric Unit (5, 41)
No.NameCountTypeFull Name
1A2M2Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2CA33Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
5IU2Mod. Residue5-IODOURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1A2M1Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
5IU-1Mod. Residue5-IODOURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1A2M1Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
5IU-1Mod. Residue5-IODOURIDINE-5'-MONOPHOSPHATE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA B:22 , A B:59BINDING SITE FOR RESIDUE CA B 93
02AC2SOFTWAREA E:22 , A E:59BINDING SITE FOR RESIDUE CA E 93
03AC3SOFTWAREGTP B:1 , C D:21BINDING SITE FOR RESIDUE CA D 22
04AC4SOFTWAREC A:21 , GTP E:1BINDING SITE FOR RESIDUE CA A 22
05AC5SOFTWAREU E:38 , G E:39 , U E:43BINDING SITE FOR RESIDUE CA E 94
06AC6SOFTWAREU B:38 , G B:39 , U B:43BINDING SITE FOR RESIDUE CA B 95
07AC7SOFTWAREA E:59BINDING SITE FOR RESIDUE CA E 96
08AC8SOFTWAREA B:59 , HOH B:240BINDING SITE FOR RESIDUE CA B 96
09AC9SOFTWAREA E:28BINDING SITE FOR RESIDUE CA E 97
10BC1SOFTWAREU B:53BINDING SITE FOR RESIDUE CA B 98
11BC2SOFTWAREG E:19 , G E:21BINDING SITE FOR RESIDUE CA E 98
12BC3SOFTWAREGTP B:1BINDING SITE FOR RESIDUE CA B 99
13BC4SOFTWAREA E:28BINDING SITE FOR RESIDUE CA E 99
14BC5SOFTWAREU E:58BINDING SITE FOR RESIDUE CA E 100
15BC6SOFTWAREC B:35 , A B:36 , LYS C:96BINDING SITE FOR RESIDUE CA B 101
16BC7SOFTWAREG E:47 , G E:48 , CA E:102BINDING SITE FOR RESIDUE CA E 101
17BC8SOFTWAREG E:48 , U E:49 , CA E:101BINDING SITE FOR RESIDUE CA E 102
18BC9SOFTWAREU E:37 , HOH E:247BINDING SITE FOR RESIDUE CA E 104
19CC1SOFTWAREG B:6 , A B:7BINDING SITE FOR RESIDUE CA B 104
20CC2SOFTWAREHOH E:251BINDING SITE FOR RESIDUE CA F 101
21CC3SOFTWAREA E:15 , C E:16BINDING SITE FOR RESIDUE CA E 105
22CC4SOFTWAREG B:48BINDING SITE FOR RESIDUE CA B 105
23CC5SOFTWAREC B:82BINDING SITE FOR RESIDUE CA B 106
24CC6SOFTWAREG B:19 , HOH B:298BINDING SITE FOR RESIDUE CA B 107
25CC7SOFTWARELYS F:23 , LYS F:27 , LEU F:44 , VAL F:45BINDING SITE FOR RESIDUE CL F 103
26CC8SOFTWARELYS F:23 , ARG F:47 , HOH F:285BINDING SITE FOR RESIDUE CL F 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M5K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M5K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M5K)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
208-282
  2C:10-89
F:10-89
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
208-282
  1-
F:10-89
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
 
208-282
  1C:10-89
-
-

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002435631ENSE00001052136chr19:41256779-41257386608SNRPA_HUMAN1-25252C:6-25
F:6-25
20
20
1.2ENST000002435632ENSE00000707951chr19:41263237-41263409173SNRPA_HUMAN25-82582C:25-82
F:25-82
58
58
1.3ENST000002435633ENSE00000707956chr19:41265336-41265515180SNRPA_HUMAN83-142602C:83-97
F:83-97
15
15
1.4ENST000002435634ENSE00000707961chr19:41268806-41268979174SNRPA_HUMAN143-200580--
1.5ENST000002435635ENSE00000842333chr19:41269492-4126958089SNRPA_HUMAN201-230300--
1.6ENST000002435636ENSE00000842334chr19:41270913-41271290378SNRPA_HUMAN230-282530--

(-) 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:RNA  Length:21
                                                    
                  1m5k A  1 GGCCACCUGACaGUCCuCUCC 21
                                    10 |    | 20 
                                      12-A2M|    
                                           17-IU 

Chain B from PDB  Type:RNA  Length:92
                                                                                                                           
                  1m5k B  1 gGAGAGAGAAGUCAACCAGAGAAACACACCAACCCAUUGCACUCCGGGUUGGUGGUAUAUUACCUGGUACGGGGGAAACUUCGUGGUGGCCG 92
                            |       10        20        30        40        50        60        70        80        90  
                            |                                                                                           
                            1-GTP                                                                                       

Chain C from PDB  Type:PROTEIN  Length:92
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:92
                                    15        25        35        45        55        65        75        85        95  
           SNRPA_HUMAN    6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
               SCOP domains d1m5kc_ C: Splicesomal U1A protein                                                           SCOP domains
               CATH domains 1m5kC00 C:6-97  [code=3.30.70.330, no name defined]                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeee.........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: C:10-89 UniProt: 10-89                                                -------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:6-2---------------------------------------------------------Exon 1.3        Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: C:25-82 UniProt: 25-82                     --------------- Transcript 1 (2)
                  1m5k C  6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
                                    15        25        35        45        55        65        75        85        95  

Chain D from PDB  Type:RNA  Length:21
                                                    
                  1m5k D  1 GGCCACCUGACaGUCCuCUCC 21
                                    10 |    | 20 
                                      12-A2M|    
                                           17-IU 

Chain E from PDB  Type:RNA  Length:92
                                                                                                                           
                  1m5k E  1 gGAGAGAGAAGUCAACCAGAGAAACACACCAACCCAUUGCACUCCGGGUUGGUGGUAUAUUACCUGGUACGGGGGAAACUUCGUGGUGGCCG 92
                            |       10        20        30        40        50        60        70        80        90  
                            |                                                                                           
                            1-GTP                                                                                       

Chain F from PDB  Type:PROTEIN  Length:92
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:92
                                    15        25        35        45        55        65        75        85        95  
           SNRPA_HUMAN    6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
               SCOP domains d1m5kf_ F: Splicesomal U1A protein                                                           SCOP domains
               CATH domains 1m5kF00 F:6-97  [code=3.30.70.330, no name defined]                                          CATH domains
           Pfam domains (1) ------RRM_1-1m5kF01 F:12-83                                                   -------------- Pfam domains (1)
           Pfam domains (2) ------RRM_1-1m5kF02 F:12-83                                                   -------------- Pfam domains (2)
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeeee........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: F:10-89 UniProt: 10-89                                                -------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: F:6-2---------------------------------------------------------Exon 1.3        Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: F:25-82 UniProt: 25-82                     --------------- Transcript 1 (2)
                  1m5k F  6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97
                                    15        25        35        45        55        65        75        85        95  

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: RRM (206)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain C,F   (SNRPA_HUMAN | P09012)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030619    U1 snRNA binding    Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA).
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0017069    snRNA binding    Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
    GO:0035614    snRNA stem-loop binding    Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
    GO:0005685    U1 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U1.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SNRPA_HUMAN | P090121aud 1drz 1dz5 1fht 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1urn 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2a3j 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4prf 4w90 4w92 4yb1 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

1m5k THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE
1m5o THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE
1m5p THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE
1m5v THE SAME RIBOZYME WITH DIFFERENT SUBSTRATE