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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BAZ2A PHD ZINC FINGER IN COMPLEX WITH UNMODIFIED H3 10-MER
 
Authors :  A. Amato, M. S. Gadd, A. Bortoluzzi, A. Ciulli
Date :  08 Sep 16  (Deposition) - 05 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,G
Biol. Unit 1:  A,G  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D,E  (1x)
Biol. Unit 5:  A,C,G  (1x)
Biol. Unit 6:  B,D,E  (1x)
Keywords :  Phd Zinc Fingers, Histone3, Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bortoluzzi, A. Amato, X. Lucas, M. Blank, A. Ciulli
Structural Basis Of Molecular Recognition Of Helical Histon H3 Tail By Phd Finger Domains.
Biochem. J. V. 474 1633 2017
PubMed-ID: 28341809  |  Reference-DOI: 10.1042/BCJ20161053

(-) Compounds

Molecule 1 - BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: PHD DOMAIN, 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, TIP5,HWALP3
 
Molecule 2 - HISTONE H3.1
    Chains: E, G
    Engineered: YES
    Fragment: UNP RESIDUES 2-11
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE H3/L
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEG
Biological Unit 1 (1x): A    G
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    DE 
Biological Unit 5 (1x): A C  G
Biological Unit 6 (1x):  B DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
3ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO4-1Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO4-1Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
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
03AC3SOFTWAREARG A:1707 , HOH A:1904 , HOH A:1912 , HOH A:1913 , HOH A:1917binding site for residue PO4 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
06AC6SOFTWAREARG B:1707 , HOH B:1910binding site for residue PO4 B 1803
07AC7SOFTWARECYS C:1679 , CYS C:1682 , HIS C:1702 , CYS C:1705binding site for residue ZN C 1801
08AC8SOFTWARECYS C:1694 , CYS C:1697 , CYS C:1720 , CYS C:1723binding site for residue ZN C 1802
09AC9SOFTWAREARG C:1707 , HOH C:1920binding site for residue GOL C 1803
10AD1SOFTWARECYS D:1679 , CYS D:1682 , HIS D:1702 , CYS D:1705binding site for residue ZN D 1801
11AD2SOFTWARECYS D:1694 , CYS D:1697 , CYS D:1720 , CYS D:1723binding site for residue ZN D 1802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T8R)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:1707 -Pro A:1708
2Arg B:1707 -Pro B:1708
3Arg C:1707 -Pro C:1708
4Arg D:1707 -Pro D:1708

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T8R)

(-) Exons   (0, 0)

(no "Exon" information available for 5T8R)

(-) 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:54
                                                                                       
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eee......eee.hhh.............hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                5t8r A 1675 NKVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQQV 1728
                                  1684      1694      1704      1714      1724    


Chain B from PDB  Type:PROTEIN  Length:51
                                                                                    
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eee......eee.hhh.............hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                5t8r B 1676 KVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQ 1726
                                  1685      1695      1705      1715      1725 


Chain C from PDB  Type:PROTEIN  Length:53
                                                                                      
               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
                5t8r C 1675 NKVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQQ 1727
                                  1684      1694      1704      1714      1724   


Chain D from PDB  Type:PROTEIN  Length:54
                                                                                       
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ................eee......eee.................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                5t8r D 1675 NKVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGDWFCTVCLAQQV 1728
                                  1684      1694      1704      1714      1724    


Chain E from PDB  Type:PROTEIN  Length:7
                                        
               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
                5t8r E    1 ARTKQTA    7


Chain G from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                5t8r G    1 ARTKQTAR    8
   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 5T8R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T8R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T8R)

(-) Gene Ontology  (43, 49)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAZ2A_HUMAN | Q9UIF9: 4lz2 4q6f 4qbm 4qf2 5agq 5mgj 5mgk 5mgl 5mgm
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5tbn 5tdr 5tdw 5v21 5v22 5va6

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