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(-) Description

Title :  CRYSTAL STRUCTURE OF AF9 YEATS BOUND TO H3K9AC PEPTIDE
 
Authors :  H. Li, Y. Li, H. Wang, Y. Ren
Date :  02 Jun 14  (Deposition) - 05 Nov 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcription, Complex, Histone Modification, Immunoglobin Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, H. Wen, Y. Xi, K. Tanaka, H. Wang, D. Peng, Y. Ren, Q. Jin, S. Y. Dent W. Li, H. Li, X. Shi
Af9 Yeats Domain Links Histone Acetylation To Dot1L-Mediate H3K79 Methylation.
Cell V. 159 558 2014
PubMed-ID: 25417107  |  Reference-DOI: 10.1016/J.CELL.2014.09.049

(-) Compounds

Molecule 1 - PROTEIN AF-9
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: YEATS DOMAIN (UNP RESIDUES 1-138)
    Gene: MLLT3, AF9, YEATS3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALL1-FUSED GENE FROM CHROMOSOME 9 PROTEIN,MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA TRANSLOCATED TO CHROMOSOME 3 PROTEIN,YEATS DOMAIN-CONTAINING PROTEIN 3
 
Molecule 2 - ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR
    Chains: B, D
    Engineered: YES
    Fragment: UNP RESIDUES 2-12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
2EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37binding site for residue EDO A 201
2AC2SOFTWAREHIS C:54 , LEU C:55 , LYS C:63binding site for residue EDO C 201
3AC3SOFTWAREGLU C:86binding site for residue EDO C 202
4AC4SOFTWAREARG C:37binding site for residue EDO C 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:69 -Pro A:70
2Glu A:94 -Pro A:95
3Pro C:69 -Pro C:70
4Glu C:94 -Pro C:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TMP)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeee..........eeeeeeeehhhhhhhhh.eeeeeee........eeee....eeeeeee...eeeeeeeee.......eeeeeeee.........eeeeeeeeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tmp A   1 MASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               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
                 4tmp B   3 TKQTARkST  11
                                  |  
                                  9-ALY


Chain C from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeee..........eeeeeeeehhhhhhhhh.eeeeeee........eeee....eeeeeee...eeeeeeeee.......eeeeeeee.........eeeeeeeeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmp C   0 HMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA 138
                                     9        19        29        39        49        59        69        79        89        99       109       119       129         


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               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
                 4tmp D   3 TKQTARkST  11
                                  |  
                                  9-ALY
   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 4TMP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 39)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AF9_HUMAN | P42568: 2lm0 2mv7 2n4q 2ndf 2ndg 5hjb 5hjd
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5kdm 5x7x

(-) Related Entries Specified in the PDB File

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