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(-) Description

Title :  PHD-TYPE ZINC FINGER OF HUMAN PHD FINGER PROTEIN 13
 
Authors :  R. Lam, C. B. Bian, C. Xu, J. Kania, C. Bountra, J. Weigelt, C. H. Arrowsmi A. M. Edwards, A. Bochkarev, J. Min, Structural Genomics Consortiu
Date :  29 Jul 10  (Deposition) - 29 Sep 10  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Phf13, Structural Genomics Consortium, Sgc, Structural Genomics, Phd- Type Zinc Finger, Protein Binding, Zinc Ion Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Chung, C. Xu, A. Fuchs, A. Mund, M. Lange, H. Staege, T. Schubert, C. Bian, I. Dunkel, A. Eberharter, C. Regnard, H. Klinker, D. Meierhofer, L. Cozzuto, A. Winterpacht, L. Di Croce, J. Min, H. Will, S. Kinkley
Phf13 Is A Molecular Reader And Transcriptional Co-Regulato Of H3K4Me2/3.
Elife V. 5 2016
PubMed-ID: 27223324  |  Reference-DOI: 10.7554/ELIFE.10607

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 13
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21-(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PHD-TYPE ZINC FINGER (UNP RESIDUES 232-281)
    Gene: PHF13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3 , HOH A:9 , HOH A:12 , GLU A:248 , ASN A:250 , ARG A:264 , GLU A:270 , PHE A:272BINDING SITE FOR RESIDUE GOL A 400
2AC2SOFTWAREHOH A:16 , HOH A:24 , TYR A:228 , MET A:246BINDING SITE FOR RESIDUE GOL A 401
3AC3SOFTWARECYS A:235 , CYS A:237 , HIS A:257 , CYS A:260BINDING SITE FOR RESIDUE ZN A 500
4AC4SOFTWARECYS A:249 , CYS A:252 , CYS A:274 , CYS A:277BINDING SITE FOR RESIDUE ZN A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O70)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O70)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O70)

(-) Exons   (0, 0)

(no "Exon" information available for 3O70)

(-) 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:55
 aligned with PHF13_HUMAN | Q86YI8 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:82
                                   209       219       229       239       249       259       269       279  
          PHF13_HUMAN   200 IVRQGKQVVFRDEDSTGNDEDIMVDSDDDSWDLVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDSK 281
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------PHD-3o70A01 A:234-280                          - Pfam domains
         Sec.struct. author .....---------------------------..............eee......eee................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3o70 A 227 LYFQG---------------------------LVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDSK 281
                                |    -         -         -  |    239       249       259       269       279  
                              231                         232
   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 3O70)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O70)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: zf-FYVE-PHD (57)
(-)
Family: PHD (44)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHF13_HUMAN | Q86YI8)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0007076    mitotic chromosome condensation    The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3o70
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 Related Entries

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        PHF13_HUMAN | Q86YI8: 3o7a

(-) Related Entries Specified in the PDB File

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