Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SPLSM3
 
Authors :  S. M. Jiang, D. H. Wu, H. W. Song
Date :  12 Apr 12  (Deposition) - 13 Jun 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1:  A,B,C,D,E,F,G  (1x)
Biol. Unit 2:  H,I,J,K,L,M,N  (1x)
Keywords :  Sm Fold, Mrna Decay, Lsm Proteins, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Wu, S. M. Jiang, M. W. Bowler, H. W. Song
Crystal Structures Of Lsm3, Lsm4 And Lsm5/6/7 From Schizosaccharomyces Pombe.
Plos One V. 7 36768 2012
PubMed-ID: 22615807  |  Reference-DOI: 10.1371/JOURNAL.PONE.0036768

(-) Compounds

Molecule 1 - PROBABLE U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3
    Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM3, SPBC9B6.05C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972

 Structural Features

(-) Chains, Units

  1234567891011121314
Asymmetric Unit : ABCDEFGHIJKLMN
Biological Unit 1 (1x): ABCDEFG       
Biological Unit 2 (1x):        HIJKLMN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 28)

Asymmetric Unit (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4EMG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EMG)

(-) 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:71
                                                                                                      
               SCOP domains d4emga_ A: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg A  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain B from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgb_ B: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg B  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain C from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgc_ C: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg C  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain D from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgd_ D: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg D  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain E from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emge_ E: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg E  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain F from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgf_ F: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg F  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain G from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgg_ G: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg G  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain H from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgh_ H: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg H  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain I from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgi_ I: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg I  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain J from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgj_ J: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg J  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain K from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgk_ K: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg K  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain L from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgl_ L: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg L  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain M from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgm_ M: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg M  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70                       


Chain N from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains d4emgn_ N: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4emg N  9 EPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNmVLGDAEEIVTTIRKHYEmLFVRGDSVILIAPPRN 93
                                    18        28        38      | 48      ||72    |   82        92 
                                                               45-MSE    55|     77-MSE            
                                                                          70
   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, 14)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4emg)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4emg)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4emg
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LSM3_SCHPO | Q9Y7M4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LSM3_SCHPO | Q9Y7M4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4EMG)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4EMG)