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 8TH C2H2 TYPE ZINC FINGER DOMAIN OF ZINC FINGER PROTEIN 347
 
Authors :  K. Masuda, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  C2H2, Zinc Finger Domain, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Masuda, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The 8Th C2H2 Type Zinc Finger Domain Of Zinc Finger Protein 347
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 347
    Chains: A
    Engineered: YES
    Expression System Plasmid: P070115-13
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER DOMAIN
    Gene: ZNF347, ZNF1111
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: ZINC FINGER PROTEIN 1111

 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 2EQ0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EQ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EQ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EQ0)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZN347_HUMAN291-311
319-339
347-367
375-395
403-423
431-451
459-479
487-507
515-535
543-563
571-591
599-619
655-675
683-703
711-731
739-759
767-787		  2-
-
-
-
-
-
A:459-479
-
A:490-490
-
-
-
-
-
-
-
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003341972aENSE00001733228chr19:53657052-5365698667ZN347_HUMAN1-550--
1.3ENST000003341973ENSE00001705088chr19:53652620-53652494127ZN347_HUMAN6-48430--
1.4bENST000003341974bENSE00001298405chr19:53652062-53651934129ZN347_HUMAN48-91440--
1.5bENST000003341975bENSE00001425913chr19:53645809-536426483162ZN347_HUMAN91-8397491A:445-490 (gaps)151

(-) 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 ZN347_HUMAN | Q96SE7 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:151
                                   378       388       398       408       418       428       438       448       458       468       478       488       498       508       518 
          ZN347_HUMAN   369 GEKPYKCNECGKAFRARSSLAIHQATHSGEKPYKCNECGKVFTQNSHLTNHWRIHTGEKPYKCNECGKAFGVRSSLAIHLVIHTGEKPYKCHECGKVFRRNSHLARHQLIHTGEKPYKCNECGKAFRAHSNLTTHQVIHTGEKPYKCNECG 519
               SCOP domains -----------------------------------------------------------------------------------d2eq0a1 A:452-479           ---------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------------------...-------------------------..--------------------------.....ee......ee.hhhhhhhhhh.......-----------------------..--.----... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_ PROSITE
               Transcript 1 Exon 1.5b  PDB: A:445-490 (gaps) UniProt: 91-839 [INCOMPLETE]                                                                                           Transcript 1
                 2eq0 A 445 GS-------------------------SGS-------------------------SG--------------------------TGEKPYKCHECGKVFRRNSHLARHQLIHTGEKP-----------------------SG--P----SSG 490
                             |       -         -       449         -         -     ||  -         -         -   |   458       468       478     |   -         -       485|  |   489 
                             |                       447 |                       450|                        452                             484                     485|  |  488  
                           446                         449                        451                                                                                 486  |       
                                                                                                                                                                         487
   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 2EQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EQ0)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (ZN347_HUMAN | Q96SE7)
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.
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 2eq0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2eq0)
 

(-) 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
  2eq0
    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
  ZN347_HUMAN | Q96SE7
    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
  ZN347_HUMAN | Q96SE7
    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
        ZN347_HUMAN | Q96SE7: 2ema 2emp 2en4 2ene 2enf 2eoe 2eow 2eq1 2eq2 2eq3 2yti 2ytk 2ytn 2ytr 2yu8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EQ0)