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(-) Description

Title :  CRYSTAL STRUCTURE OF A SIGNAL RECOGNITION PARTICLE ALU DOMAIN IN THE ELONGATION ARREST CONFORMATION
 
Authors :  L. Bousset, C. Mary, M. A. Brooks, A. Scherrer, K. Strub, S. Cusack
Date :  01 Sep 14  (Deposition) - 05 Nov 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B,C,D,R,S
Biol. Unit 1:  C,D,S  (1x)
Biol. Unit 2:  A,B,R  (1x)
Keywords :  Signaling Protein, Signal Recognition Particle, Translation, Rna Folding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bousset, C. Mary, M. A. Brooks, A. Scherrer, K. Strub, S. Cusack
Crystal Structure Of A Signal Recognition Particle Alu Domain In The Elongation Arrest Conformation.
Rna V. 20 1955 2014
PubMed-ID: 25336584  |  Reference-DOI: 10.1261/RNA.047209.114

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH9
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET9A
    Fragment: RESIDUES 1-85
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP9
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH14DELTAR
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET9A
    Fragment: RESIDUES 1-107
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP14,18 KDA ALU RNA-BINDING PROTEIN
 
Molecule 3 - SRP RNA
    Chains: R, S
    Fragment: ALU DOMAIN, RESIDUES 1-89 AND RESIDUES 289-314
    Organism Scientific: PYROCOCCUS HORIKOSHII OT3
    Organism Taxid: 70601
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDRS
Biological Unit 1 (1x):   CD S
Biological Unit 2 (1x): AB  R 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1CCC2Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4UYJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UYJ)

(-) 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:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....eeeeeee....eeeeeee....eee......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 4uyj A   2 PQYQTWEEFSRAAEKLYLADPmKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLmRLmVA  75
                                    11        21 |      31        41        51        61        71 |  
                                                23-MSE                                         70-MSE 
                                                                                                  73-MSE


Chain B from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhh.....eeeeeeee..........eeeeeee....eeeeeehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4uyj B   1 mVLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPPADNKCLLRATDGKKKISTVVSSKEVNKFQmAYSNLLRANmDG  93
                            |       10        20        30        51        61        71        81        91  
                            |                                    39|                            81-MSE    91-MSE
                            1-MSE                                 51                                          


Chain C from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....eeeeee......eeeeee....eeeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 4uyj C   2 PQYQTWEEFSRAAEKLYLADPmKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLmRLmVA  75
                                    11        21 |      31        41        51        61        71 |  
                                                23-MSE                                         70-MSE 
                                                                                                  73-MSE


Chain D from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhh.......eeeeeeee..........eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4uyj D   1 mVLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPPADNKCLLRATDGKKKISTVVSSKEVNKFQmAYSNLLRANmDGL  94
                            |       10        20        30        51        61        71        81        91   
                            |                                    39|                            81-MSE    91-MSE
                            1-MSE                                 51                                           


Chain R from PDB  Type:RNA  Length:110
                                                                                                                                              
                 4uyj R   6 GGGGCUAGGCCGGGGGGUUCGGCGUCCCCUGUAACCGGAAACCGCCGAUAUGCCGGGGCCGAAGCCCGAGGGGCGGUUCCCGUAAGGGUUCCCACCCUCGGGCGUGCCUc 115
                                    15        25        35        45        55        65        75        85        95       105       115
                                                                                                                                       115-CCC


Chain S from PDB  Type:RNA  Length:110
                                                                                                                                              
                 4uyj S   6 GGGGCUAGGCCGGGGGGUUCGGCGUCCCCUGUAACCGGAAACCGCCGAUAUGCCGGGGCCGAAGCCCGAGGGGCGGUUCCCGUAAGGGUUCCCACCCUCGGGCGUGCCUc 115
                                    15        25        35        45        55        65        75        85        95       105       115
                                                                                                                                       115-CCC
   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 4UYJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 29)

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  SRP09_HUMAN | P49458
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  SRP14_HUMAN | P37108
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 Related Entries

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

UniProtKB/Swiss-Prot
        SRP09_HUMAN | P49458: 1e8o 1e8s 1ry1 4uyk 5aox
        SRP14_HUMAN | P37108: 1e8o 1e8s 1ry1 4uyk 5aox

(-) Related Entries Specified in the PDB File

4uyk CRYSTAL STRUCTURE OF A SIGNAL RECOGNITION PARTICLE ALU DOMAIN IN THE ELONGATION ARREST CONFORMATION