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(-) Description

Title :  CRYSTAL STRUCTURE OF LSM2-8 COMPLEX, SPACE GROUP P21
 
Authors :  L. Zhou, J. Hang, Y. Zhou, R. Wan, G. Lu, C. Yan, Y. Shi
Date :  12 Aug 13  (Deposition) - 13 Nov 13  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
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 LSM8
    Chains: A, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM8, YJR022W, J1464, YJR83.16
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2
    Chains: B, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM2, SMX5, SNP3, YBL026W, YBL0425
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SMALL NUCLEAR RIBONUCLEOPROTEIN D HOMOLOG SNP3
 
Molecule 3 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3
    Chains: C, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM3, SMX4, USS2, YLR438C-A
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SMX4 PROTEIN
 
Molecule 4 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6
    Chains: D, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM6, YDR378C, D9481.18
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 5 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5
    Chains: E, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM5, YER146W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 6 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7
    Chains: F, M
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM7, YNL147W, N1202, N1780
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 7 - U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4
    Chains: G, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LSM4, SDB23, USS1, YER112W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4M78)

(-) Sites  (0, 0)

(no "Site" information available for 4M78)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M78)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M78)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M78)

(-) Exons   (0, 0)

(no "Exon" information available for 4M78)

(-) 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:67
                                                                                                   
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeee....eeeeeeeee.....eeeeeeee.....eeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 4m78 A   1 MSATLKDYLNKRVVIILVDGESLIASLNGFDKNTNLFLTNVFNRISKEFISKAQLLRGSEIALVGLI  67
                                    10        20        30        40        50        60       


Chain B from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains d4m78b_ B: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee....eeeeeeeee.....eeeeeee...........eee....eeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4m78 B   1 MLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISSTYPHLGSVRNIFIRGSTVRYVYLNKNMVDTNLLQDATRREVM  91
                                    10        20        30        40     || 54        64        74        84       
                                                                        46|                                        
                                                                         51                                        


Chain C from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains d4m78c_ C: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeeee....eeeeeeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4m78 C   3 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHSNIVLSDAVETIYQLNNEELSESERRSEMVFIRGDTVTLISTP  79
                                    12        22        32        42        52        62        72       


Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4m78d_ D: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee........eee...eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4m78 D  10 SVTTEFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESNNNKLLNKFNSDVFLRGTQVMYISEQ  84
                                    19        29        39        49        59        69        79     


Chain E from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains d4m78e_ E: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee...eeeeeeeee......eeeeeeeeee...eeeee...eeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4m78 E   6 ILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDNEKVMQHHGRMLLSGNNIAILVPG  84
                                    15        25        35        45        61        71        81   
                                                                           54|                       
                                                                            61                       


Chain F from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains d4m78f_ F: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeee...eee..eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4m78 F  27 ILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYMNARKLGLTVIRGTILVSLSSA 105
                                    36        46        56        66   ||   90       100     
                                                                      70|                    
                                                                       85                    


Chain G from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m78g_ G: automated matches                                           SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee....eeeeeeeee.....eeeeeeeee..eeeeeee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4m78 G   1 MLPLYLLTNAKGQQMQIELKNGEIIQGILTNVDNWMNLTLSNVTEYSVKLNEIYIRGTFIKFIKLQDNII  86
                                    10        20        30        40      ||66        76        86
                                                                         47|                      
                                                                          64                      


Chain H from PDB  Type:PROTEIN  Length:67
                                                                                                   
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeee....eeeeeeeee.....eeeeeeee....eeeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 4m78 H   1 MSATLKDYLNKRVVIILVDGESLIASLNGFDKNTNLFLTNVFNRISKEFISKAQLLRGSEIALVGLI  67
                                    10        20        30        40        50        60       


Chain I from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains d4m78i_ I: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....eeeeee....eeeeeeeee.....eeeeeee........eeee....eeeeee.....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4m78 I   1 MLFFSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISSPHLGSVRNIFIRGSTVRYVYLNKNMVDTNLLQDATRREVM  91
                                    10        20        30        40    ||  56        66        76        86     
                                                                       45|                                       
                                                                        52                                       


Chain J from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains d4m78j_ J: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4m78 J   3 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHSNIVLSDAVETIYQLNNEELSESERRSEMVFIRGDTVTLISTP  79
                                    12        22        32        42        52        62        72       


Chain K from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains d4m78k_ K: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee......eeeee...eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 4m78 K  11 VTTEFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESNNNKLLNKFNSDVFLRGTQVMYISEQ  84
                                    20        30        40        50        60        70        80    


Chain L from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4m78l_ L: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..eeeeee...eeeeeeeee......eeeeeeeeee...eeeee...eeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4m78 L   4 PEILPLEVIDKTINQKVLIVLQSNREFEGTLVGFDDFVNVILEDAVEWLIDNEKVMQHHGRMLLSGNNIAILVPG  84
                                    13        23        33        43        53||      69        79     
                                                                             54|                       
                                                                              61                       


Chain M from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains d4m78m_ M: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeee....eeeeeeeee.....eeeeeeeee...eee..eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4m78 M  27 ILDLAKYKDSKIRVKLMGGKLVIGVLKGYDQLMNLVLDDTVEYMNARKLGLTVIRGTILVSLSSA 105
                                    36        46        56        66   ||   90       100     
                                                                      70|                    
                                                                       85                    


Chain N from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains d4m78n_ N: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee....eeeeeeeee.....eeeeeeeee..eeeeeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4m78 N   1 MLPLYLLTNAKGQQMQIELKNGEIIQGILTNVDNWMNLTLSNVTEYSVKLNEIYIRGTFIKFIKLQDNIID  87
                                    10        20        30        40      ||66        76        86 
                                                                         47|                       
                                                                          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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M78)

(-) Gene Ontology  (28, 131)

Asymmetric Unit(hide GO term definitions)

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  4m78
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  LSM2_YEAST | P38203
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  LSM3_YEAST | P57743
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  LSM4_YEAST | P40070
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  LSM5_YEAST | P40089
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  LSM6_YEAST | Q06406
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  LSM7_YEAST | P53905
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  LSM8_YEAST | P47093
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 Related Entries

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

UniProtKB/Swiss-Prot
        LSM2_YEAST | P38203: 3jcm 4c8q 4c92 4m75 4m77 4m7a 4m7d 4n0a 5gan
        LSM3_YEAST | P57743: 3bw1 3jcm 4c8q 4c92 4m75 4m77 4m7a 4m7d 4n0a 5gan
        LSM4_YEAST | P40070: 3jcm 4c8q 4c92 4m75 4m77 4m7a 4m7d 5gan
        LSM5_YEAST | P40089: 3jcm 4c8q 4c92 4m75 4m77 4m7a 4m7d 5gan
        LSM6_YEAST | Q06406: 3jcm 4c8q 4c92 4m75 4m77 4m7a 4m7d 5gan
        LSM7_YEAST | P53905: 3jcm 4c8q 4c92 4m75 4m77 4m7a 4m7d 5gan
        LSM8_YEAST | P47093: 3jcm 4m77 4m7a 4m7d 5gan

(-) Related Entries Specified in the PDB File

4m75 4m77 4m7a 4m7d