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(-) Description

Title :  CRYSTAL STRUCTURE OF SGF29 TANDEM TUDOR DOMAIN IN COMPLEX WITH A CARBA CONTAINING PEPTIDE
 
Authors :  A. Dong, C. Xu, W. Tempel, T. Cerovina, C. Bountra, C. H. Arrowsmith, A. M J. Min, Structural Genomics Consortium (Sgc)
Date :  12 Jun 15  (Deposition) - 01 Jul 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Sgf29, Tandem Tudor Domain, Carba Containing Peptide, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Kamps, J. Huang, J. Poater, C. Xu, B. J. Pieters, A. Dong, J. Min, W. Sherman, T. Beuming, F. Matthias Bickelhaupt, H. Li, J. Mecinovic
Chemical Basis For The Recognition Of Trimethyllysine By Epigenetic Reader Proteins.
Nat Commun V. 6 8911 2015
PubMed-ID: 26578293  |  Reference-DOI: 10.1038/NCOMMS9911

(-) Compounds

Molecule 1 - SAGA-ASSOCIATED FACTOR 29 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TANDEM TUDOR DOMAIN (UNP RESIDUES 115-293)
    Gene: CCDC101, SGF29
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SGF29, COILED-COIL DOMAIN-CONTAINING PROTEIN 101
 
Molecule 2 - CARBA-CONTAINING PEPTIDE
    Chains: C, D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
14WQ2Mod. Amino Acid(2S)-2-AMINO-7,7-DIMETHYLOCTANOIC ACID
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4UNX7Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
14WQ1Mod. Amino Acid(2S)-2-AMINO-7,7-DIMETHYLOCTANOIC ACID
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
14WQ1Mod. Amino Acid(2S)-2-AMINO-7,7-DIMETHYLOCTANOIC ACID
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4UNX3Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:206 , ARG A:208 , ARG A:209 , HOH A:430binding site for residue SO4 A 301
2AC2SOFTWARESER B:206 , ARG B:208 , ARG B:209 , HOH B:512binding site for residue SO4 B 301
3AC3SOFTWAREGLN B:124 , LEU B:237 , TYR B:238 , GLN B:240 , THR B:241 , HOH B:418 , HOH B:432 , HOH B:443 , HOH B:527binding site for residue GOL B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C0M)

(-) Exons   (0, 0)

(no "Exon" information available for 5C0M)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..............................eeeeeee.....eeeeeeeeeeee....eeeeee........eeee...eee..........hhhhh.....eeeee.....eeeeeeeee........eeeee............eeehhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c0m A 114 GRRGVLMTLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVAC 287
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283    


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..............................eeeeeee.....eeeeeeeeeeee....eeeeee.......eeeee...eee..........hhhhh.....eeeee.....eeeeeeeee........eeeee............eeehhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c0m B 116 RGVLMTLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACKEPK 291
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      


Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5c0m C   1 ARTxQ   5
                               | 
                               4-4WQ


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5c0m D   1 ARTxQ   5
                               | 
                               | 
                               4-4WQ
   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 5C0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C0M)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  5c0m
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  SGF29_HUMAN | Q96ES7
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 Related Entries

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

UniProtKB/Swiss-Prot
        SGF29_HUMAN | Q96ES7: 3lx7 3me9 3mea 3met 3meu 3mev 3mew

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