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(-) Description

Title :  CRYSTAL STRUCTURE OF A PHD FINGER BOUND TO HISTONE H3 T3PH PEPTIDE
 
Authors :  H. Li, X. Zhang
Date :  13 Dec 15  (Deposition) - 04 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,C,D,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  C,F  (1x)
Keywords :  Zinc Finger Protein, Bromodomain, Transcription-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Zhang, D. Zhao, X. Xiong, Z. He, H. Li
Multifaceted Histone H3 Methylation And Phosphorylation Readout By The Plant Homeodomain Finger Of Human Nuclear Antigen Sp100C
J. Biol. Chem. V. 291 12786 2016
PubMed-ID: 27129259  |  Reference-DOI: 10.1074/JBC.M116.721159

(-) Compounds

Molecule 1 - NUCLEAR AUTOANTIGEN SP-100
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 696-878
    GeneSP100
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSP100 NUCLEAR ANTIGEN
 
Molecule 2 - PEPTIDE FROM HISTONE H3
    ChainsD, F
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCHEMICALLY SYNTHESIZED H3 PEPTIDE 1-15 WITH T3PH MODIFICATION
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ACDF
Biological Unit 1 (1x)A D 
Biological Unit 2 (1x) C F

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1TPO2Mod. Amino AcidPHOSPHOTHREONINE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TPO1Mod. Amino AcidPHOSPHOTHREONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TPO1Mod. Amino AcidPHOSPHOTHREONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:705 , CYS A:708 , HIS A:725 , CYS A:728binding site for residue ZN A 901
2AC2SOFTWARECYS A:717 , THR A:719 , CYS A:720 , CYS A:742 , CYS A:745binding site for residue ZN A 902
3AC3SOFTWARECYS C:705 , CYS C:708 , HIS C:725 , CYS C:728binding site for residue ZN C 901
4AC4SOFTWARECYS C:717 , THR C:719 , CYS C:720 , CYS C:742 , CYS C:745binding site for residue ZN C 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FB0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:730 -Pro A:731
2Asn A:738 -Pro A:739
3Ile C:730 -Pro C:731
4Asn C:738 -Pro C:739

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FB0)

(-) Exons   (0, 0)

(no "Exon" information available for 5FB0)

(-) 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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee......eee................hhhhhhhhhhh....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fb0 A 695 SDPCPENSNICEVCNKWGRLFCCDTCPRSFHEHCHIPSVEANKNPWSCIFCRIKTIQERSGHQESEVLMRQMQPEEQLKCEFLLLKVYCDSKSSFFASEPYYGPQKPMWLNKVKTSLNEQMYTRVEGFVQDMRLIFHNHKEFYREDKFTRLGIQVQDIFEKNFRNIFAIQET 877
                                   704       714       724       734       744       754|      769       779       789       799 ||    815       825       835       845       855       865       875  
                                                                                     754|                                      801|                                                                     
                                                                                      760                                       808                                                                     

Chain C from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee......eee................hhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fb0 C 695 SDPCPENSNICEVCNKWGRLFCCDTCPRSFHEHCHIPSVEANKNPWSCIFCRIKTIQERSSGHQESEVLMRQMQPEEQLKCEFLLLKVYCDSKSSFFASEPGPQKPMWLNKVKTSLNEQMYTRVEGFVQDMRLIFHNHKEFYREDKFTRLGIQVQDIFEKNFRNIFAIQE 876
                                   704       714       724       734       744       754|      768       778       788       798||     816       826       836       846       856       866       876
                                                                                     754|                                     799|                                                                    
                                                                                      759                                      808                                                                    

Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5fb0 D   1 ARtKQTARKS  10
                              |     10
                              3-TPO   

Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5fb0 F   1 ARtKQTARKS  10
                              |     10
                              3-TPO   

   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 5FB0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FB0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FB0)

(-) Gene Ontology  (70, 80)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P684311cs9 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 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 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        K7EMV3_HUMAN | K7EMV35fb1 5ffv 5gh9
        SP100_HUMAN | P234971h5p 4ptb 5fb1 5pwc 5pwd 5pwe 5pwf 5pwg 5pwh 5pwi 5pwj 5pwk 5pwl 5pwm 5pwn 5pwo 5pwp 5pwq 5pwr 5pws 5pwt 5pwu 5pwv 5pww 5pwx 5pwy 5pwz 5px0 5px1 5px2 5px3 5px4 5px5 5px6 5px7 5px8 5px9 5pxa 5pxb 5pxc 5pxd 5pxe 5pxf 5pxg 5pxh 5pxi 5pxj 5pxk 5pxl 5pxm 5pxn 5pxo 5pxp 5pxq 5pxr 5pxs 5pxt 5pxu 5pxv 5pxw 5pxx 5pxy 5pxz 5py0 5py1 5py2 5py3 5py4 5py5 5py6 5py7 5py8 5py9 5pya 5pyb 5pyc 5pyd 5pye 5pyf 5pyg 5pyh 5pyi 5pyj 5pyk 5pyl 5pym 5pyn 5pyo 5pyp 5pyq 5pyr 5pys 5pyt 5pyu 5pyv 5pyw 5pyx 5pyy 5pyz 5pz0 5pz1 5pz2 5pz3 5pz4 5pz5 5pz6 5pz7 5pz8 5pz9 5pza 5pzb 5pzc 5pzd 5pze 5pzf 5pzg 5pzh 5pzi 5pzj
UniProtKB/TrEMBL
        K7EMV3_HUMAN | K7EMV35b75 5b76 5b77 5b78

(-) Related Entries Specified in the PDB File

5fb1