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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BAZ2A PHD ZINC FINGER IN COMPLEX WITH UNMODIFIED H3K4 HISTONE PEPTIDE
 
Authors :  C. Tallant, L. Overvoorde, T. Krojer, P. Filippakopoulos, F. Von Delf C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. Ciulli, S. Knapp, Struc Genomics Consortium (Sgc)
Date :  22 Apr 14  (Deposition) - 21 May 14  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B,C,D,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,G  (1x)
Biol. Unit 3:  C,H  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Bromodomain Adjacent To Zinc Finger Domain Protein 2A, Transcription Termination Factor I-Interacting Protein 5, Ttf-I-Interacting Protein 5, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tallant, E. Valentini, O. Fedorov, L. Overvoorde, F. M. Ferguson, P. Filippakopoulos, D. I. Svergun, S. Knapp, A. Ciulli
Molecular Basis Of Histone Tail Recognition By Human Tip5 Phd Finger And Bromodomain Of The Chromatin Remodeling Complex Norc.
Structure V. 23 80 2015
PubMed-ID: 25533489  |  Reference-DOI: 10.1016/J.STR.2014.10.017

(-) Compounds

Molecule 1 - BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3) ROSETTA
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1673-1728
    Gene: BAZ2A, KIAA0314, TIP5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5, TTF-I-INTERACTING PROTEIN 5, TIP5, HWALP3
 
Molecule 2 - UNMODIFIED H3K4 PEPTIDE
    Chains: F, G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDFGH
Biological Unit 1 (1x): A   F  
Biological Unit 2 (1x):  B   G 
Biological Unit 3 (1x):   C   H
Biological Unit 4 (1x):    D   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1679 , CYS A:1682 , HIS A:1702 , CYS A:1705BINDING SITE FOR RESIDUE ZN A 1801
02AC2SOFTWARECYS A:1694 , CYS A:1697 , CYS A:1720 , CYS A:1723BINDING SITE FOR RESIDUE ZN A 1802
03AC3SOFTWARETRP A:1718 , PHE A:1719 , TRP D:1718 , PHE D:1719BINDING SITE FOR RESIDUE EDO A 1803
04AC4SOFTWARECYS B:1679 , CYS B:1682 , HIS B:1702 , CYS B:1705BINDING SITE FOR RESIDUE ZN B 1801
05AC5SOFTWARECYS B:1694 , CYS B:1697 , CYS B:1720 , CYS B:1723BINDING SITE FOR RESIDUE ZN B 1802
06AC6SOFTWAREASP B:1686 , ASN B:1687 , ASP B:1688 , ARG B:1707 , LYS B:1709BINDING SITE FOR RESIDUE EDO B 1803
07AC7SOFTWARECYS C:1679 , CYS C:1682 , HIS C:1702 , CYS C:1705BINDING SITE FOR RESIDUE ZN C 1800
08AC8SOFTWARECYS C:1694 , CYS C:1697 , CYS C:1720 , CYS C:1723BINDING SITE FOR RESIDUE ZN C 1801
09AC9SOFTWARECYS D:1679 , CYS D:1682 , HIS D:1702 , CYS D:1705BINDING SITE FOR RESIDUE ZN D 1801
10BC1SOFTWARECYS D:1694 , CYS D:1697 , CYS D:1720 , CYS D:1723BINDING SITE FOR RESIDUE ZN D 1802
11BC2SOFTWAREGLU A:1711 , GLU D:1689 , PHE D:1690 , ALA D:1712 , VAL D:1713BINDING SITE FOR RESIDUE EDO D 1803
12BC3SOFTWAREVAL A:1674 , ASN A:1675 , VAL A:1677 , GLY A:1685 , ASP A:1688 , GLU A:1689 , LEU A:1691 , LEU A:1692 , LEU A:1693 , CYS A:1694 , ASP A:1695 , VAL A:1713 , PRO A:1714 , GLU A:1715 , GLY A:1716 , LYS B:1676 , HOH F:101 , HOH F:102BINDING SITE FOR CHAIN F OF UNMODIFIED H3K4 PEPTIDE
13BC4SOFTWAREASN B:1675 , VAL B:1677 , GLY B:1685 , ASP B:1688 , GLU B:1689 , LEU B:1691 , LEU B:1692 , LEU B:1693 , CYS B:1694 , ASP B:1695 , VAL B:1713 , PRO B:1714 , GLU B:1715 , GLY B:1716 , HOH B:1913 , LYS D:1676BINDING SITE FOR CHAIN G OF UNMODIFIED H3K4 PEPTIDE
14BC5SOFTWAREVAL C:1677 , GLY C:1685 , ASP C:1688 , GLU C:1689 , LEU C:1691 , LEU C:1692 , LEU C:1693 , VAL C:1713 , PRO C:1714 , GLU C:1715 , GLY C:1716 , HOH C:1905 , ASP D:1688 , LEU D:1693BINDING SITE FOR CHAIN H OF UNMODIFIED H3K4 PEPTIDE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q6F)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Arg A:1707 -Pro A:1708
2Asn B:1675 -Lys B:1676
3Arg B:1707 -Pro B:1708
4Arg C:1707 -Pro C:1708
5Arg D:1707 -Pro D:1708

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q6F)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q6F)

(-) 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:56
                                                                                         
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........hhh.eee......eee.................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                4q6f A 1673 SVNKVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQQV 1728
                                  1682      1692      1702      1712      1722      


Chain B from PDB  Type:PROTEIN  Length:54
                                                                                       
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eee......eee.................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                4q6f B 1675 NKVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQQV 1728
                                  1684      1694      1704      1714      1724    


Chain C from PDB  Type:PROTEIN  Length:51
                                                                                    
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eee......eee.................hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                4q6f C 1676 KVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQ 1726
                                  1685      1695      1705      1715      1725 


Chain D from PDB  Type:PROTEIN  Length:53
                                                                                      
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eee......eee.................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                4q6f D 1676 KVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQQV 1728
                                  1685      1695      1705      1715      1725   


Chain F 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
                4q6f F    1 ARTKQ    5


Chain G from PDB  Type:PROTEIN  Length:5
                                      
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                4q6f G    1 ARTKQ    5


Chain H 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
                4q6f H    1 ARTK    4
   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 4Q6F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q6F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q6F)

(-) Gene Ontology  (21, 21)

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 Related Entries

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        BAZ2A_HUMAN | Q9UIF9: 4lz2 4qbm 4qf2 5agq 5mgj 5mgk 5mgl 5mgm 5t8r

(-) Related Entries Specified in the PDB File

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