Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE C2H2 TYPE ZINC FINGER (REGION 640-672) OF HUMAN ZINC FINGER PROTEIN 28 HOMOLOG
 
Authors :  T. Tomizawa, N. Tochio, H. Abe, K. Saito, H. Li, M. Sato, S. Koshiba, N. Kobayashi, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zf-C2H2, Nmr, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tochio, T. Tomizawa, H. Abe, K. Saito, H. Li, M. Sato, S. Koshiba, N. Kobayashi, T. Kigawa, S. Yokoyama
Solution Structure Of The C2H2 Type Zinc Finger (Region 640-672) Of Human Zinc Finger Protein 28 Homolog
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 28 HOMOLOG
    Chains: A
    Engineered: YES
    Expression System Plasmid: P061225-08
    Expression System Vector Type: PLASMID
    Fragment: ZF-C2H2
    Gene: ZFP28
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: ZFP-28, KRUEPPEL-LIKE ZINC FINGER FACTOR X6

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2EM3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EM3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EM3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EM3)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZFP28_HUMAN422-442
450-470
478-499
507-527
535-555
563-583
591-611
619-639
647-667
675-695
703-723
731-751
759-779
787-807		  2-
-
-
-
-
-
-
-
A:15-35
-
A:44-45
-
-
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003013181ENSE00000728674chr19:57050317-57050595279ZFP28_HUMAN1-70700--
1.2ENST000003013182ENSE00001319353chr19:57050994-5705108592ZFP28_HUMAN70-100310--
1.3ENST000003013183ENSE00001638838chr19:57058877-57059003127ZFP28_HUMAN101-143430--
1.4ENST000003013184ENSE00000728686chr19:57059176-5705927196ZFP28_HUMAN143-175330--
1.5ENST000003013185ENSE00000728690chr19:57060327-57060490164ZFP28_HUMAN175-229550--
1.6ENST000003013186ENSE00000728695chr19:57061436-57061550115ZFP28_HUMAN230-268390--
1.7ENST000003013187ENSE00000728701chr19:57061879-5706197496ZFP28_HUMAN268-300330--
1.8ENST000003013188ENSE00001290596chr19:57065053-570681693117ZFP28_HUMAN300-8685691A:1-46 (gaps)181

(-) Sequences/Alignments

NMR Structure
   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:46
 aligned with ZFP28_HUMAN | Q8NHY6 from UniProtKB/Swiss-Prot  Length:868

    Alignment length:181
                                   554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724 
          ZFP28_HUMAN   545 GSSLTVHQRIHTGEKPYECDVCRKAFSHHASLTQHQRVHSGEKPFKCKECGKAFRQNIHLASHLRIHTGEKPFECAECGKSFSISSQLATHQRIHTGEKPYECKVCSKAFTQKAHLAQHQKTHTGEKPYECKECGKAFSQTTHLIQHQRVHTGEKPYKCMECGKAFGDNSSCTQHQRLHTG 725
               SCOP domains -----------------------------------------------------------------------------------------------d2em3a1 A:8-35              ---------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...---------..-------------------------..------------------------------------------------------.....ee......ee.hhhhhhhhhhhhh....-----------------------..--.-------------..---------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZINC_FINGER-------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -- PROSITE
               Transcript 1 Exon 1.8  PDB: A:1-46 (gaps) UniProt: 300-868 [INCOMPLETE]                                                                                                                            Transcript 1
                 2em3 A   1 GSS---------GS-------------------------SG------------------------------------------------------TGEKPYECKVCSKAFTQKAHLAQHQKTHTGEKP-----------------------SG--P-------------SS---------G  46
                              |      -  ||     -         -         6|        -         -         -         -         -     |  12        22        32       | -         -         - ||  |   -        44|        -|
                              3         4|                         6|                                                      8                              40                      41| 43            44|        46
                                         5                          7                                                                                                              42                45
   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  (1, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EM3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EM3)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (ZFP28_HUMAN | Q8NHY6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2em3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2em3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2em3
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ZFP28_HUMAN | Q8NHY6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ZFP28_HUMAN | Q8NHY6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ZFP28_HUMAN | Q8NHY6: 2em2 2em4 2emj 2emk 2eml 2en9 2enh 2eoh 2ep0 2epx 2epz 2ytm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EM3)