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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   HADDOCK MODEL OF MYT1 F4F5 - DNA COMPLEX

Authors :   R. Gamsjaeger, M. R. O'Connell, L. Cubeddu, N. E. Shepherd, J. A. Lowry, M. Vandevenne, M. K. Swanton, J. M. Matthews, J. P. Mackay

Date :   08 Oct 13 (Deposition) - 06 Nov 13 (Release) - 25 Dec 13 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C
NMR Structure *: A,B,C  (1x)

Keywords :   Myt1, Zinc Finger, Metal Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Gamsjaeger, M. R. O'Connell, L. Cubeddu, N. E. Shepherd, J. A. Lowry A. H. Kwan, M. Vandevenne, M. K. Swanton, J. M. Matthews, J. P. Mackay
A Structural Analysis Of Dna Binding By Myelin Transcriptio Factor 1 Double Zinc Fingers.
J. Biol. Chem. V. 288 35180 2013
PubMed-ID: 24097990 | Reference-DOI: 10.1074/JBC.M113.482075

Molecule 1 - MYELIN TRANSCRIPTION FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 792-880
	Gene	:	MYT1, KIAA0835, NZF2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MYT1, NEURAL ZINC FINGER FACTOR 2, NZF-2

*Molecule 2 - DNA (5'-D(APCPCPGPAPAPAPGPTPTPCPAPC)-3')**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(GPTPGPAPAPCPTPTPTPCPGPGPT)-3')**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3
NMR Structure	:	A	B	C
NMR Structure * (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

NMR Structure * (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:802 , THR A:804 , CYS A:807 , HIS A:820 , CYS A:826	BINDING SITE FOR RESIDUE ZN A 901
2	AC2	SOFTWARE	CYS A:846 , THR A:848 , CYS A:851 , HIS A:864 , CYS A:870	BINDING SITE FOR RESIDUE ZN A 902

(no "SS Bond" information available for 2MF8)

(no "Cis Peptide Bond" information available for 2MF8)

(no "SAP(SNP)/Variant" information available for 2MF8)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_CCHHC	PS51802	Zinc finger CCHHC-type profile.	MYT1_MOUSE	21-64 435-478 479-522 793-836 837-880 886-929 939-982	1	- - - - A:837-873 - -

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_CCHHC	PS51802	Zinc finger CCHHC-type profile.	MYT1_MOUSE	21-64 435-478 479-522 793-836 837-880 886-929 939-982	1	- - - - A:837-873 - -

(no "Exon" information available for 2MF8)

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:75
 aligned with MYT1_MOUSE | Q8CFC2 from UniProtKB/Swiss-Prot  Length:1127

    Alignment length:75
                                   808       818       828       838       848       858       868     
           MYT1_MOUSE   799 LLTCPTPGCDGSGHITGNYASHRSLSGCPLADKSLRNLMAAHSADLKCPTPGCDGSGHITGNYASHRSLSGCPRA 873
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_CCHHC  PDB: - UniProt: 793-836     ZF_CCHHC  PDB: A:837-873              PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2mf8 A 799 LLTCPTPGCDGSGHITGNYASHRSLSGCPLADKSLRNLMAAHSADLKCPTPGCDGSGHITGNYASHRSLSGCPRA 873
                                   808       818       828       838       848       858       868

Chain B from PDB  Type:DNA  Length:13
                                             
                 2mf8 B   1 ACCGAAAGTTCAC  13
                                    10

Chain C from PDB  Type:DNA  Length:13
                                             
                 2mf8 C  14 GTGAACTTTCGGT  26
                                    23

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 '\|'

(no "SCOP Domain" information available for 2MF8)

(no "CATH Domain" information available for 2MF8)

(no "Pfam Domain" information available for 2MF8)

NMR Structure(hide GO term definitions)

Chain A (MYT1_MOUSE | Q8CFC2)

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:0001158	enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0001678	cellular glucose homeostasis	A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment.
	GO:0060539	diaphragm development	The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs.
	GO:0031018	endocrine pancreas development	The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
	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:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0009791	post-embryonic development	The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
	GO:0032350	regulation of hormone metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone.
	GO:0061178	regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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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	MYT1_MOUSE \| Q8CFC2	:	2jx1 2jyd

2jyd	HADDOCK STARTING STRUCTURE

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