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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   LMO4-LIM2 IN COMPLEX WITH DEAF1 (404-418)

Authors :   S. Joseph, J. M. Matthews, A. H. -Y. Kwan, J. P. Mackay, L. Cubeddu, P. Foo

Date :   06 Aug 13 (Deposition) - 20 Aug 14 (Release) - 20 Aug 14 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Lmo4, Deaf1, Transcription, Embryonic Development, Cancer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Joseph, A. H. Kwan, P. Foo, L. Cubeddu, J. P. Mackay, J. M. Matthews
Structural Characterisation Of Lim-Only Protein 4 (Lmo4) In Complex With Deformed Epidermal Autoregulatory Factor-1 (Deaf1)
To Be Published
PubMed: search

Molecule 1 - FUSION PROTEIN OF LIM DOMAIN TRANSCRIPTION FACTOR LMO4 (77- 147) AND DEAF1 (404-418)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LMO4 (UNP RESIDUES 77-147), DEAF1 (UNP RESIDUES 404-418)
	Gene	:	LMO4
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

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:87 , CYS A:90 , HIS A:109 , CYS A:112	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS A:115 , CYS A:118 , CYS A:137 , ASP A:140	BINDING SITE FOR RESIDUE ZN A 1002

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

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

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

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_2	PS50023	LIM domain profile.	LMO4_MOUSE	21-83 85-147	1	- A:85-147
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LMO4_MOUSE	23-57 87-122	1	- A:87-122

NMR Structure * (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIM_DOMAIN_2	PS50023	LIM domain profile.	LMO4_MOUSE	21-83 85-147	1	- A:85-147
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LMO4_MOUSE	23-57 87-122	1	- A:87-122

(no "Exon" information available for 2MBV)

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:96
 aligned with DEAF1_MOUSE | Q9Z1T5 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:206
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412      
          DEAF1_MOUSE   213 GTLYKSRLGSGGRGRCIKQGENWYSPTEFEAMAGRASSKDWKRSIRYAGRPLQCLIQDGILNPHAASCTCAACCDDMTLSGPVRLFVPYKRRKKENELPTTPVKKDSPKNITLLPATAATTFTVTPSGQITTSGALTFDRASTVEATAVISESPAQGDVFAGATVQEAGVQPPCRVGHPEPHYPGYQDSCQIAPFPEAALPTSHPK 418
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-.........--......----........eee....eee---------....-------------.......------------------------------------.....---..eeee.-------.eeee...---.......-.....---...----------------------------....ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mbv A   1 GS-YIRLFGNSG--ACSACG----QSIPASELVMRAQGNVYH---------LKCF-------------TCSTCRN------------------------------------RLVPG---DRFHYIN-------GSLFCEHD---RPTALIN-GGSGG---SGS----------------------------IAPFPEAALPTSHPK 418
                             | |    83 |  |   91    |   97       107 |       - |  |    -       115    |    -         -         -         - |   | 126     |   -   |   139|   |  146| |   |  -| |      -         -         - |     412      
                             2 |      85 86   91   92              109       110  |           114   120                                  121 125 126   132     133    140 141   147 | 205 206 |                          404              
                              77                                                113                                                                                               201       208

Chain A from PDB  Type:PROTEIN  Length:96
 aligned with LMO4_MOUSE | P61969 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:113
                                                                                                                           155   156         
                                    67        77        87        97       107       117       127       137       147       | -   |   162   
           LMO4_MOUSE    58 GDIGTSCYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSLQS-----NPLLPDQKVC 165
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------.......................eee....eee..................eeee..eeee......................ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LIM_DOMAIN_2  PDB: -      -LIM_DOMAIN_2  PDB: A:85-147 UniProt: 85-147                    ----------------------- PROSITE (1)
                PROSITE (2) -----------------------------LIM_DOMAIN_1  PDB: A:87-122         ------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2mbv A   1 GS-----------------YIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGGSGGSGSIAPFPEAALPTSHPK 418
                             |       -        77        87        97       107       117       127       137       147|      405       415   
                             2                77                                                                   147|    208|              
                                                                                                                    201     404

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 2MBV)

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

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

NMR Structure(hide GO term definitions)

Chain A (DEAF1_MOUSE | Q9Z1T5)

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: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:0001662	behavioral fear response	An acute behavioral change resulting from a perceived external threat.
	GO:0048706	embryonic skeletal system development	The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
	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: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: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:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	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:0033599	regulation of mammary gland epithelial cell proliferation	Any process that modulates the frequency, rate or extent of mammary gland epithelial cell proliferation.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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.
	GO:0008542	visual learning	Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain A (LMO4_MOUSE | P61969)

molecular function
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0031333	negative regulation of protein complex assembly	Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
	GO:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	GO:0033674	positive regulation of kinase activity	Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0050865	regulation of cell activation	Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
	GO:0042659	regulation of cell fate specification	Any process that mediates the adoption of a specific fate by a cell.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0021527	spinal cord association neuron differentiation	The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of association neurons. Association neurons are cells located in the dorsal portion of the spinal cord that integrate sensory input. Differentiation includes the processes involved in commitment of a cell to a specific fate.
	GO:0021522	spinal cord motor neuron differentiation	The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate.
	GO:0048538	thymus development	The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
	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.
	GO:0021514	ventral spinal cord interneuron differentiation	The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of ventral spinal cord interneurons. Ventral spinal cord interneurons are cells located in the ventral portion of the spinal cord that transmit signals between sensory and motor neurons and are required for reflexive responses. Differentiation includes the processes involved in commitment of a cell to a specific fate.
	GO:0003281	ventricular septum development	The progression of the ventricular septum over time from its formation to the mature structure.
cellular component
	GO:0031252	cell leading edge	The area of a motile cell closest to the direction of movement.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

NMR Structure
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	LMO4_MOUSE \| P61969
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UniProtKB/Swiss-Prot
	LMO4_MOUSE \| P61969	:	1m3v 1rut 2dfy

1rut	LMO4 LIM1+LIM2 IN COMPLEX WITH LDB1
2l4z	LMO4 LIM1 IN COMPLEX WITH CTIP RELATED ID: 19415 RELATED DB: BMRB

Description

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Ligands, Modified Residues, Ions (1, 2)

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