1Y7Q - JenaLib

Title :   MAMMALIAN SCAN DOMAIN DIMER IS A DOMAIN-SWAPPED HOMOLOGUE OF THE HIV CAPSID C-TERMINAL DOMAIN

Authors :   D. Ivanov, J. R. Stone, J. L. Maki, T. Collins, G. Wagner

Date :   09 Dec 04 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Scan Domain; Retroviral Capsid C-Terminal Domain; Dimer; C2H2 Zinc Finger Associated, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Ivanov, J. R. Stone, J. L. Maki, T. Collins, G. Wagner
Mammalian Scan Domain Dimer Is A Domain-Swapped Homolog Of The Hiv Capsid C-Terminal Domain
Mol. Cell V. 17 137 2005
PubMed-ID: 15629724 | Reference-DOI: 10.1016/J.MOLCEL.2004.12.015
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

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
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Chain A from PDB  Type:PROTEIN  Length:98
 aligned with ZN174_HUMAN | Q15697 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:101
                                    41        51        61        71        81        91       101       111       121       131 
          ZN174_HUMAN    32 GPPLQKNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPPEIQARVRHRCPMSSKEIVTLVEDFHRASKKPK 132
               SCOP domains -----d1y7qa1 A:37-132 Zinc finger protein 174                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---......hhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SCAN_BOX  PDB: A:46-126 UniProt: 46-126                                          ------ PROSITE
               Transcript 1 Exon 1.1b  PDB: A:35-132 (gaps) UniProt: 1-134 [INCOMPLETE]                                           Transcript 1
                 1y7q A  35 GS---KNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDFHRASKKPK 132
                             |   |  41        51        61        71        81        91       101       111       121       131 
                             |  37                                                                                               
                            36

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with ZN174_HUMAN | Q15697 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:101
                                    41        51        61        71        81        91       101       111       121       131 
          ZN174_HUMAN    32 GPPLQKNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPPEIQARVRHRCPMSSKEIVTLVEDFHRASKKPK 132
               SCOP domains d1   y7qb_ B: Zinc finger protein 174                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------SCAN-1y7qB01 B:40-132                                                                         Pfam domains (1)
           Pfam domains (2) --------SCAN-1y7qB02 B:40-132                                                                         Pfam domains (2)
         Sec.struct. author ..---......hhhhhhhh..........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SCAN_BOX  PDB: B:46-126 UniProt: 46-126                                          ------ PROSITE
               Transcript 1 Exon 1.1b  PDB: B:35-132 (gaps) UniProt: 1-134 [INCOMPLETE]                                           Transcript 1
                 1y7q B  35 GS---KNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDFHRASKKPK 132
                             |   |  41        51        61        71        81        91       101       111       121       131 
                            36  37

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, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (15, 15)

NMR Structure(hide GO term definitions)

Chain A,B (ZN174_HUMAN | Q15697)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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