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(-) Description

Title :  NMR STRUCTURE OF THE ZFY-6T[Y10L] ZINC FINGER
 
Authors :  M. J. Lachenmann, J. E. Ladbury, N. B. Phillips, N. Narayana, X. Qian, M. A. Weiss
Date :  12 Dec 01  (Deposition) - 13 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Zinc Finger, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Lachenmann, J. E. Ladbury, N. B. Phillips, N. Narayana, X. Qian, M. A. Weiss
The Hidden Thermodynamics Of A Zinc Finger.
J. Mol. Biol. V. 316 969 2002
PubMed-ID: 11884136  |  Reference-DOI: 10.1006/JMBI.2001.5335
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER Y-CHROMOSOMAL PROTEIN
    Chains: A
    Engineered: YES
    Mutation: YES
    Other Details: THIS PEPTIDE WAS SYNTHESIZED BY SOLID-PHASE SYNTHESIS. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:5 , CYS A:8 , HIS A:21 , HIS A:26BINDING SITE FOR RESIDUE ZN A 31

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KLS)

(-) Cis Peptide Bonds  (7, 12)

NMR Structure
No.ModelResidues
13, 4Ala A:13 -Asp A:14
24, 6, 25Ser A:15 -Ser A:16
313His A:26 -Ser A:27
422, 24Lys A:1 -Thr A:2
523Ser A:16 -Asn A:17
625, 30Glu A:29 -Lys A:30
726Lys A:19 -Thr A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KLS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KLS)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003830521bENSE00001803243Y:2803322-2803487166ZFY_HUMAN-00--
1.3ENST000003830523ENSE00002197402Y:2821950-282203889ZFY_HUMAN1-21210--
1.4bENST000003830524bENSE00001661706Y:2829115-2829687573ZFY_HUMAN21-2121920--
1.5ENST000003830525ENSE00001774385Y:2843136-2843285150ZFY_HUMAN212-262510--
1.6ENST000003830526ENSE00001719392Y:2843552-2843695144ZFY_HUMAN262-310490--
1.7ENST000003830527ENSE00001649504Y:2844711-2844863153ZFY_HUMAN310-361520--
1.8cENST000003830528cENSE00001777381Y:2845981-2846121141ZFY_HUMAN361-408480--
1.9cENST000003830529cENSE00001494540Y:2846851-28505473697ZFY_HUMAN408-8013941A:1-3030

(-) 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 ZFY_HUMAN | P08048 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:30
                                   579       589       599
            ZFY_HUMAN   570 KPYQCQYCEYRSADSSNLKTHIKTKHSKEM 599
               SCOP domains d1klsa_ A: ZFY                 SCOP domains
               CATH domains ------------------------------ CATH domains
           Pfam domains (1) ----------------zf-H2C2_2-1kl- Pfam domains (1)
           Pfam domains (2) ----------------zf-H2C2_2-1kl- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
               Transcript 1 Exon 1.9c  PDB: A:1-30         Transcript 1
                 1kls A   1 KTYQCQYCELRSADSSNLKTHIKTKHSKEK  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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1KLS)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: C2H2-zf (71)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (ZFY_HUMAN | P08048)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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: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: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: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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  1kls
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 Related Entries

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

UniProtKB/Swiss-Prot
        ZFY_HUMAN | P08048: 1klr 1xrz 5znf 7znf

(-) Related Entries Specified in the PDB File

1klr 1KLR CONTAINS THE Y10F MUTANT
5znf 5ZNF CONTAINS THE WILD-TYPE ZFY-6T ZINC FINGER