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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TDRD1 EXTENDED TUDOR DOMAIN IN COMPLEX WITH A SYMMETRICALLY DIMETHYLATED E2F PEPTIDE
 
Authors :  C. Tallant, P. Savitsky, J. Moehlenbrink, C. Chan, G. Nunez-Alonso, J. F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, O. Fedorov, Thangue, S. Knapp, Structural Genomics Consortium (Sgc)
Date :  01 Nov 16  (Deposition) - 16 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna-Mediated Gene Silencing, Structural Genomics, Structural Genomics Consortium, Sgc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tallant, P. Savitsky, J. Moehlenbrink, C. Chan, G. Nunez-Alonso, J. A. Newman, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra O. Fedorov, N. B. La Thangue, S. Knapp
Crystal Structure Of Human Tdrd1 Extended Tudor Domain In Complex With A Symmetrically Dimethylated E2F Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TDRD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CANCER/TESTIS ANTIGEN 41.1,CT41.1
 
Molecule 2 - E2F PEPTIDE
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: 2MR: DIMETHYLATED ARGININE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (1x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
12MR3Mod. Amino AcidN3, N4-DIMETHYLARGININE
2EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12MR2Mod. Amino AcidN3, N4-DIMETHYLARGININE
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12MR1Mod. Amino AcidN3, N4-DIMETHYLARGININE
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:537 , ASP A:538 , PHE A:539 , LEU A:586 , MET A:587binding site for residue EDO A 701
2AC2SOFTWARETYR A:575binding site for residue EDO A 702
3AC3SOFTWAREHIS B:501 , PHE B:551 , TYR B:558 , TYR B:575 , TYR B:578 , ASN B:580binding site for residue 2MR B 701
4AC4SOFTWAREGLY B:574 , TYR B:575binding site for residue EDO B 702
5AC5SOFTWAREHIS A:501 , PHE A:551 , TYR A:558 , TYR A:575 , TYR A:578 , ASN A:580 , GLY C:9binding site for Di-peptide GLY C 7 and 2MR C 8
6AC6SOFTWAREHIS A:501 , PHE A:551 , ASP A:554 , TYR A:558 , TYR A:575 , TYR A:578 , ASN A:580 , GLY C:7 , 2MR C:10binding site for Di-peptide 2MR C 8 and GLY C 9
7AC7SOFTWAREGLU A:553 , ASP A:554 , GLN A:556 , TYR A:558 , 2MR C:8binding site for Di-peptide GLY C 9 and 2MR C 10

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:530 -A:590
2B:530 -B:590

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile B:483 -Pro B:484

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M9N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M9N)

(-) Exons   (0, 0)

(no "Exon" information available for 5M9N)

(-) 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:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh...........eeeeeeeeeee..eeeeee..hhhhhhhhhhhhhhhhhh.............eeeee......eeeeeeeeeee..eeeeee.....eeeee...ee..hhhhhh.....eeeee..eee.....hhhhhhhhhhhhh...eeeeeeee....eeeeeee......eehhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m9n A 474 NIVVDKSDLIPKVLTLNVGDEFCGVVAHIQTPEDFFCQQLQSGRKLAELQASLSKYCDQLPPRSDFYPAIGDICCAQFSEDDQWYRASVLAYASEESVLVGYVDYGNFEILSLMRLCPIIPKLLELPMQAIKCVLAGVKPSLGIWTPEAICLMKKLVQNKIITVKVVDKLENSSLVELIDKSETPHVSVSKVLLDAGFAVGE 675
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673  


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh...........eeeeeeeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhh............eeeee......eeeeeeeeeee..eeeeee.....eeeee...ee..hhhhhh.....eeeee..........hhhhhhhhhhhhh...eeeeeeee....eeeeeee....eehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m9n B 473 NNIVVDKSDLIPKVLTLNVGDEFCGVVAHIQTPEDFFCQQLQSGRKLAELQASLSKYCDQLPPRSDFYPAIGDICCAQFSEDDQWYRASVLAYASEESVLVGYVDYGNFEILSLMRLCPIIPKLLELPMQAIKCVLAGVKPSLGIWTPEAICLMKKLVQNKIITVKVVDKLENSSLVELIDKSEHVSVSKVLLDAGFA 672
                                   482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652   ||  664        
                                                                                                                                                                                                                 656|             
                                                                                                                                                                                                                  659             


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 5m9n C   7 GxGx  10
                             | |
                             8-2MR
                              10-2MR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5M9N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M9N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M9N)

(-) Gene Ontology  (57, 60)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        E2F1_HUMAN | Q01094: 1h24 1o9k 2aze 5m9o

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