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(-) Description

Title :  COMPLEX STRUCTURE OF THE ZF-CW DOMAIN AND THE H3K4ME3 PEPTIDE
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Mar 10  (Deposition) - 15 Sep 10  (Release) - 29 Sep 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Zf-Cw Domain, Zcwpw1, Zinc-Finger, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal-Binding Protein-Nuclear Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. He, T. Umehara, K. Saito, T. Harada, S. Watanabe, T. Yabuki, T. Kigawa, M. Takahashi, K. Kuwasako, K. Tsuda, T. Matsuda, M. Aoki, E. Seki, N. Kobayashi, P. Guntert, S. Yokoyama, Y. Muto
Structural Insight Into The Zinc Finger Cw Domain As A Histone Modification Reader
Structure V. 18 1127 2010
PubMed-ID: 20826339  |  Reference-DOI: 10.1016/J.STR.2010.06.012

(-) Compounds

Molecule 1 - ZINC FINGER CW-TYPE PWWP DOMAIN PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHSIS
    Expression System PlasmidP060116-12
    Expression System Vector TypePLASMID
    FragmentZF-CW DOMAIN, RESIDUES 246-307
    GeneZCWPW1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsE. COLI - CELL FREE
    SynonymZF-CW
 
Molecule 2 - HISTONE H3
    ChainsB
    EngineeredYES
    FragmentHISTONE H3 TAIL, UNP RESIDUES 2-11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsH3K4ME3 PEPTIDE
    Other Details - SourceCHEMICAL SYNTHESIZED, PURCHASED
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN1Ligand/IonZINC ION
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:259 , CYS A:264 , CYS A:285 , CYS A:296BINDING SITE FOR RESIDUE ZN A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RR4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RR4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RR4)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CWPS51050 Zinc finger CW-type profile.ZCPW1_HUMAN250-304  1A:250-304
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CWPS51050 Zinc finger CW-type profile.ZCPW1_HUMAN250-304  1A:250-304

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003980271bENSE00001481569chr7:99999664-99999512153ZCPW1_HUMAN491-542520--
1.2dENST000003980272dENSE00001898404chr7:99998959-99998476484ZCPW1_HUMAN542-6481070--
1.3cENST000003980273cENSE00001350589chr7:100026302-100026191112ZCPW1_HUMAN-00--
1.4ENST000003980274ENSE00001350580chr7:100022759-100022653107ZCPW1_HUMAN-00--
1.5ENST000003980275ENSE00002160830chr7:100018301-10001824557ZCPW1_HUMAN1-10100--
1.6bENST000003980276bENSE00001640354chr7:100017506-100017253254ZCPW1_HUMAN10-94850--
1.7bENST000003980277bENSE00001632533chr7:100016812-10001673479ZCPW1_HUMAN95-121270--
1.8cENST000003980278cENSE00001626549chr7:100014806-100014689118ZCPW1_HUMAN121-160400--
1.9ENST000003980279ENSE00000977558chr7:100014079-100013928152ZCPW1_HUMAN160-211520--
1.10bENST0000039802710bENSE00001404216chr7:100013717-100013598120ZCPW1_HUMAN211-251411A:239-251 (gaps)36
1.11bENST0000039802711bENSE00000824847chr7:100007167-100007051117ZCPW1_HUMAN251-290401A:251-29040
1.12bENST0000039802712bENSE00000824848chr7:100006282-100006162121ZCPW1_HUMAN290-330411A:290-30718
1.13ENST0000039802713ENSE00000709058chr7:100004926-10000485176ZCPW1_HUMAN330-355260--
1.14ENST0000039802714ENSE00000709059chr7:100004421-100004317105ZCPW1_HUMAN356-390350--
1.15ENST0000039802715ENSE00000824852chr7:100002716-10000263681ZCPW1_HUMAN391-417270--
1.16ENST0000039802716ENSE00000824853chr7:100001867-10000180167ZCPW1_HUMAN418-440230--
1.17bENST0000039802717bENSE00000824854chr7:100001408-10000131792ZCPW1_HUMAN440-470310--
1.18ENST0000039802718ENSE00001180416chr7:100000199-10000013961ZCPW1_HUMAN471-491210--

(-) 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:69
 aligned with ZCPW1_HUMAN | Q9H0M4 from UniProtKB/Swiss-Prot  Length:648

    Alignment length:92
                                   225       235       245       255       265       275       285       295       305  
          ZCPW1_HUMAN   216 KTQGGHEHRQEDRLKKTVQDHSQIRDQQKGEISGFGQCLVWVQCSFPNCGKWRRLCGNIDPSVLPDNWSCDQNTDVQYNRCDIPEETWTGLE 307
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------zf-CW-2rr4A01 A:254-303                           ---- Pfam domains
         Sec.struct. author ....-----------------------.............eee........eee......hhh......hhh...hhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ZF_CW  PDB: A:250-304 UniProt: 250-304                 --- PROSITE
           Transcript 1 (1) Exon 1.10b  PDB: A:239-251 (gaps)   --------------------------------------Exon 1.12b         Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.11b  PDB: A:251-290              ----------------- Transcript 1 (2)
                 2rr4 A 239 GSSG-----------------------SSGEISGFGQCLVWVQCSFPNCGKWRRLCGNIDPSVLPDNWSCDQNTDVQYNRCDIPEETWTGLE 307
                               |     -         -       245       255       265       275       285       295       305  
                             242                     243                                                                

Chain B from PDB  Type:PROTEIN  Length:10
 aligned with A8K4Y7_HUMAN | A8K4Y7 from UniProtKB/TrEMBL  Length:136

    Alignment length:10
                                    11
         A8K4Y7_HUMAN     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2rr4 B   1 ARTkQTARKS  10
                               |    10
                               |      
                               4-M3L  

   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 2RR4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RR4)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (ZCPW1_HUMAN | Q9H0M4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.

Chain B   (A8K4Y7_HUMAN | A8K4Y7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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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 Related Entries

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        ZCPW1_HUMAN | Q9H0M42e61

(-) Related Entries Specified in the PDB File

2e61 FREE STATE STRUCTURE OF ZF-CW