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(-) Description

Title :  CRYSTAL STRUCTURE OF LSM1-7 COMPLEX
 
Authors :  L. Zhou, J. Hang, Y. Zhou, R. Wan, G. Lu, C. Yan, Y. Shi
Date :  12 Aug 13  (Deposition) - 23 Oct 13  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
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 Like Protein, Rna Splicing, Structural Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zhou, J. Hang, Y. Zhou, R. Wan, G. Lu, P. Yin, C. Yan, Y. Shi
Crystal Structures Of The Lsm Complex Bound To The 3' End Sequence Of U6 Small Nuclear Rna.
Nature V. 506 116 2014
PubMed-ID: 24240276  |  Reference-DOI: 10.1038/NATURE12803

(-) Compounds

Molecule 1 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1
    ChainsA, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLSM1, SPB8, YJL124C, J0714
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 2 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2
    ChainsB, I
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLSM2, SMX5, SNP3, YBL026W, YBL0425
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 3 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3
    ChainsC, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLSM3, SMX4, USS2, YLR438C-A
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 4 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6
    ChainsD, K
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 5 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5
    ChainsE, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLSM5, YER146W
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 6 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7
    ChainsF, M
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 7 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4
    ChainsG, N
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C

 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  (2, 41)

Asymmetric Unit (2, 41)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE39Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 19)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE B:1 , PHE B:4BINDING SITE FOR RESIDUE CL B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M75)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M75)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M75)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M75)

(-) Exons   (0, 0)

(no "Exon" information available for 4M75)

(-) 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:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhh....eeeeee....eeeeeeeee.....eeeeeeee..ee....ee..eeeeeeee....eeeeee...........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m75 A  32 DLYLDQYNFTTTAAIVSSVDRKIFVLLRDGRmLFGVLRTFDQYANLILQDCVERIYFSEENKYAEEDRGIFmIRGENVVmLGEVDIDKEDQPLmERIPFKEAWLTKQKNDEKRFKEETHKGKKmARHGIVYDFHKSDmY 172
                                    41        51        61 |      71        81        91       101 |     111       121  ||   133       143       153   |   163       | 
                                                          63-MSE                                 103-MSE 111-MSE      124|                           157-MSE       171-MSE
                                                                                                                       127-MSE                                         

Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains d4m75b_ B: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee....eeeeeeeee.....eee...ee..............eee....eeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4m75 B   1 mLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISSTDEKKYPHLGSVRNIFIRGSTVRYVYLNKNmVDTNLLQDATRREVm  91
                            |       10        20        30        40        50        60        70     |  80        90|
                            |                                                                         76-MSE         91-MSE
                            1-MSE                                                                                      

Chain C from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m75c_ 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
                 4m75 C   4 PLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHSNIVLSDAVETIYQSESERRSEmVFIRGDTVTLISTP  79
                                    13        23        33        43      ||59     |  69        79
                                                                         50|      65-MSE          
                                                                          57                      

Chain D from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains d4m75d_ D: automated matches                                             SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh..eeeeee....eeeeeeeee.....eeeeeeeee.........ee....eee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 4m75 D  14 EFLSDIIGKTVNVKLASGLLYSGRLESIDGFmNVALSSATEHYESNNNKLLNKFNSDVFLRGTQVmYISEQK  85
                                    23        33        43 |      53        63        73     |  83  
                                                          45-MSE                            79-MSE  

Chain E from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4m75e_ E: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeeee.....eeeee...eeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4m75 E   6 ILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDSRNEKVmQHHGRmLLSGNNIAILVPG  84
                                    15        25        35        45        59     |  69 |      79     
                                                                           54|     |     |             
                                                                            59     |     |             
                                                                                  65-MSE |             
                                                                                        71-MSE         

Chain F from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4m75f_ F: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeeee...ee...ee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4m75 F  16 RKKFEGPREAILDLAKYKDSKIRVKLmGGKLVIGVLKGYDQLmNLVLDDTVEYmSARKLGLTVIRGTILVSLSSA 105
                                  ||26        36      | 46        56  |     66   |||  90       100     
                                 22|                 43-MSE          59-MSE     70-MSE                 
                                  24                                             71|                   
                                                                                  86                   

Chain G from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains d4m75g_ G: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh...eeeeee....eeeeeeeee.....eeeeeeee......eeee....eeeeee..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4m75 G  -6 NLYFQGSmLPLYLLTNAKGQQmQIELKNGEIIQGILTNVDNWmNLTLSNVTEYSVKLNEIYIRGTFIKFIKLQDNIIDKVKQ  91
                                   | 3        13 |      23        33  |     43   ||   69        79        89  
                                   1-MSE        15-MSE               36-MSE     47|                           
                                                                                 64                           

Chain H from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.....eeeeee....eeeeeeeee.....eeeeeeeee.......ee.eeeeeeeee....eeeeeeehhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m75 H  38 YNFTTTAAIVSSVDRKIFVLLRDGRmLFGVLRTFDQYANLILQDCVERIYFSEENKYAEEDRGIFmIRGENVVmLGEVDIDKEDQPLEAmERIPFKEAWLTKQKNDEKRFKEETHKGKKmARHGIVYDFHKSDm 171
                                    47        57     |  67        77        87        97     | 107   |   117       127       137       147       157       167   |
                                                    63-MSE                                 103-MSE 111-MSE         127-MSE                       157-MSE       171-MSE

Chain I from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains d4m75i_ I: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeee.....eeeeeeeee.....eeeeeeee....hhhh.eeeeee.hhhh.eee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4m75 I   1 mLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISSTDKYPHLGSVRNIFIRGSTVRYVYLNKNmVDTNLLQDATRR  88
                            |       10        20        30        40      ||52        62        72   |    82      
                            |                                            47|                        76-MSE        
                            1-MSE                                         50                                      

Chain J from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4m75j_ J: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeeeee...eeeeeeeee......eeeeeeeeeeee....ee..eeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4m75 J   3 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHSNIVLSDAVETIYQLEELSESERRSEmVFIRGDTVTLISTP  79
                                    12        22        32        42        54        64|       74     
                                                                           51|         65-MSE          
                                                                            54                         

Chain K from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains d4m75k_ K: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeee.....eeeeeeeee.....eeeeeeeee.....ee...eeee.hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4m75 K  10 SVTTEFLSDIIGKTVNVKLASGLLYSGRLESIDGFmNVALSSATEHYEKLLNKFNSDVFLRGTQVmYISEQ  84
                                    19        29        39     |  49       |63        73     |  83 
                                                              45-MSE      57|               79-MSE 
                                                                           62                      

Chain L from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4m75l_ L: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee....eeeeeeeee.....eeeeeeeeee....eeeeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4m75 L   6 ILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDRNEKVmQHHGRmLLSGNNIAILVPGG  85
                                    15        25        35        45        60    |   70|       80     
                                                                           54|    |     |              
                                                                            60    |     |              
                                                                                 65-MSE |              
                                                                                       71-MSE          

Chain M from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains d4m75m_ M: automated matches                                   SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeee....eeeeeeeee.....eeeeeeeee....ee..eee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 4m75 M  29 DLAKYKDSKIRVKLmGGKLVIGVLKGYDQLmNLVLDDTVEYmSARKLGLTVIRGTILVSLSS 104
                                    38    |   48        58|       68 |||    92       102  
                                         43-MSE          59-MSE     70-MSE                
                                                                     71|                  
                                                                      86                  

Chain N from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains d4m75n_ N: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh...eeeeee....eeeeeeeee.....eee..........eee....eeeeee.....hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4m75 N  -7 ENLYFQGSmLPLYLLTNAKGQQmQIELKNGEIIQGILTNVDNWmNLTLSNVTEVKLNEIYIRGTFIKFIKLQDNIIDKVKQQ  92
                                    |2        12  |     22        32   |    42  ||    70        80        90  
                                    1-MSE        15-MSE               36-MSE   45|                            
                                                                                64                            

   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  (2, 12)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M75)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M75)

(-) Gene Ontology  (34, 131)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LSM1_YEAST | P470174c8q 4c92
        LSM2_YEAST | P382033jcm 4c8q 4c92 4m77 4m78 4m7a 4m7d 4n0a 5gan
        LSM3_YEAST | P577433bw1 3jcm 4c8q 4c92 4m77 4m78 4m7a 4m7d 4n0a 5gan
        LSM4_YEAST | P400703jcm 4c8q 4c92 4m77 4m78 4m7a 4m7d 5gan
        LSM5_YEAST | P400893jcm 4c8q 4c92 4m77 4m78 4m7a 4m7d 5gan
        LSM6_YEAST | Q064063jcm 4c8q 4c92 4m77 4m78 4m7a 4m7d 5gan
        LSM7_YEAST | P539053jcm 4c8q 4c92 4m77 4m78 4m7a 4m7d 5gan

(-) Related Entries Specified in the PDB File

4m77 4m78 4m7a 4m7d