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 - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF MIZ-1 ZINC FINGER 5
 
Authors :  D. Bernard, M. Bedard, J. Bilodeau, P. Lavigne
Date :  24 Oct 12  (Deposition) - 14 Nov 12  (Release) - 27 Apr 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  C2H2 Zinc Fingers, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Bernard, M. Bedard, J. Bilodeau, P. Lavigne
Nmr Structure Note: Structure Of Miz-1 Zinc Fingers 5 To 7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 17
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 STAR (DE3)
    Expression System Taxid469008
    Expression System VectorPET-3A
    FragmentC2H2-TYPE 5-8, ZINC FINGER RESIDUES 416-526
    GeneMIZ1, ZBTB17, ZNF151, ZNF60
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMYC-INTERACTING ZINC FINGER PROTEIN 1, MIZ-1, ZINC FINGER PROTEIN 151, ZINC FINGER PROTEIN 60

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , CYS A:9 , HIS A:22 , HIS A:26BINDING SITE FOR RESIDUE ZN A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M0D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M0D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M0D)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZBT17_HUMAN308-328
336-356
364-384
392-412
420-440
448-468
476-496
504-524
530-552
560-580
588-608
616-637
719-739
  1-
-
-
-
A:6-26
-
-
-
-
-
-
-
-
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZBT17_HUMAN308-328
336-356
364-384
392-412
420-440
448-468
476-496
504-524
530-552
560-580
588-608
616-637
719-739
  1-
-
-
-
A:6-26
-
-
-
-
-
-
-
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003757431bENSE00001839520chr1:16302621-16302478144ZBT17_HUMAN-00--
1.2ENST000003757432ENSE00001348924chr1:16299620-1629953487ZBT17_HUMAN-00--
1.4ENST000003757434ENSE00002171255chr1:16274992-16274786207ZBT17_HUMAN1-69690--
1.6bENST000003757436bENSE00001695578chr1:16273618-16273430189ZBT17_HUMAN69-132640--
1.7bENST000003757437bENSE00001722255chr1:16272789-16272649141ZBT17_HUMAN132-179480--
1.7hENST000003757437hENSE00001738306chr1:16272335-16272210126ZBT17_HUMAN179-221430--
1.8bENST000003757438bENSE00001755221chr1:16271697-16271432266ZBT17_HUMAN221-309890--
1.9ENST000003757439ENSE00001602262chr1:16271334-16271192143ZBT17_HUMAN310-357480--
1.10bENST0000037574310bENSE00001684066chr1:16271095-16270795301ZBT17_HUMAN357-4571011A:1-3030
1.10iENST0000037574310iENSE00000751342chr1:16270390-1627030388ZBT17_HUMAN458-487300--
1.10kENST0000037574310kENSE00000751341chr1:16270210-16270094117ZBT17_HUMAN487-526400--
1.11bENST0000037574311bENSE00000751340chr1:16270014-16269894121ZBT17_HUMAN526-566410--
1.11fENST0000037574311fENSE00000751339chr1:16269689-16269559131ZBT17_HUMAN566-610450--
1.13aENST0000037574313aENSE00000751338chr1:16269233-16269024210ZBT17_HUMAN610-680710--
1.13eENST0000037574313eENSE00002146007chr1:16268915-1626882690ZBT17_HUMAN680-710310--
1.14bENST0000037574314bENSE00001653173chr1:16268747-16268364384ZBT17_HUMAN710-803940--

(-) 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:30
 aligned with ZBT17_HUMAN | Q13105 from UniProtKB/Swiss-Prot  Length:803

    Alignment length:30
                                   424       434       444
          ZBT17_HUMAN   415 EKPYQCDYCGRSFSDPTSKMRHLETHDTDK 444
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ...ee......ee.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -----ZINC_FINGER_C2H2_1   ---- PROSITE
               Transcript 1 Exon 1.10b  PDB: A:1-30        Transcript 1
                 2m0d A   1 MKPYQCDYCGRSFSDPTSKMRHLETHDTDK  30
                                    10        20        30

   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 2M0D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M0D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M0D)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (ZBT17_HUMAN | Q13105)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0007398    ectoderm development    The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.
    GO:0001702    gastrulation with mouth forming second    A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    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: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.

 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
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2m0d)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2m0d
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ZBT17_HUMAN | Q13105
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ZBT17_HUMAN | Q13105
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ZBT17_HUMAN | Q131052lvr 2lvt 2lvu 2m0e 2m0f 2n25 2n26 2q81 3m52 4u2m 4u2n 5ion

(-) Related Entries Specified in the PDB File

2lvr MIZ-1 ZINC FINGER DOMAIN 8
2lvt MIZ-1 ZINC FINGER DOMAIN 9
2lvu MIZ-1 ZINC FINGER DOMAIN 10
2m0e MIZ-1 ZINC FINGER DOMAIN 6
2m0f RELATED ID: 18806 RELATED DB: BMRB