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Title :   CRYSTAL STRUCTURE OF A CYCLIZED PROTEIN FUSION OF LMO4 LIM DOMAINS 1 AND 2 WITH THE LIM INTERACTING DOMAIN OF LDB1

Authors :   C. M. J. Jeffries, S. C. Graham, C. A. Collyer, J. M. Guss, J. M. Matthews

Date :   06 Mar 06 (Deposition) - 31 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : C,X
Biol. Unit 1: X  (1x)
Biol. Unit 2: C  (1x)

Keywords :   Zinc Finger, Lim Only Protein, Lim Domain, Circular Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. J. Jeffries, S. C. Graham, P. H. Stokes, C. A. Collyer, J. M. Guss, J. M. Matthews
Stabilization Of A Binary Protein Complex By Intein-Mediate Cyclization
Protein Sci. V. 15 2612 2006
PubMed-ID: 17001033 | Reference-DOI: 10.1110/PS.062377006

Molecule 1 - FUSION PROTEIN OF LIM DOMAIN TRANSCRIPTION FACTOR LMO4 AND LIM DOMAIN-BINDING PROTEIN 1
	Chains	:	X, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNW1120, PCY76
	Expression System Strain	:	BL21(DE3) RECA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LMO4
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	CYCLISED FUSION OF LMO4 RESIDUES 18-152 TO LDB1 LID RESIDUES 300-339 VIA TWO FLEXIBLE LINKERS WITH SEQUENCE GGSGGSGGSGG AND TRESGSIEF
	Synonym	:	CZ-FLINC4

		1	2
Asymmetric Unit	:	C	X
Biological Unit 1 (1x)	:		X
Biological Unit 2 (1x)	:	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS X:23 , CYS X:26 , HIS X:44 , CYS X:47	BINDING SITE FOR RESIDUE ZN X 601
02	AC2	SOFTWARE	CYS X:50 , CYS X:53 , CYS X:73 , ASP X:76	BINDING SITE FOR RESIDUE ZN X 602
03	AC3	SOFTWARE	CYS X:115 , CYS X:118 , CYS X:137 , ASP X:140	BINDING SITE FOR RESIDUE ZN X 603
04	AC4	SOFTWARE	CYS X:87 , CYS X:90 , HIS X:109 , CYS X:112	BINDING SITE FOR RESIDUE ZN X 604
05	AC5	SOFTWARE	CYS C:23 , CYS C:26 , HIS C:44 , CYS C:47	BINDING SITE FOR RESIDUE ZN C 601
06	AC6	SOFTWARE	CYS C:50 , CYS C:53 , CYS C:73 , ASP C:76	BINDING SITE FOR RESIDUE ZN C 602
07	AC7	SOFTWARE	CYS C:115 , CYS C:118 , CYS C:137 , ASP C:140	BINDING SITE FOR RESIDUE ZN C 603
08	AC8	SOFTWARE	CYS C:87 , CYS C:90 , HIS C:109 , CYS C:112	BINDING SITE FOR RESIDUE ZN C 604
09	AC9	SOFTWARE	ARG C:22 , GLY C:28 , LYS C:29 , ARG X:79 , HOH X:697	BINDING SITE FOR RESIDUE GOL C 501
10	BC1	SOFTWARE	ARG C:79 , HOH C:696 , ARG X:22 , GLY X:28 , LYS X:29	BINDING SITE FOR RESIDUE GOL X 502

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

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

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

Asymmetric Unit (2, 8)

	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	4	C:21-83 X:21-83 C:85-146 X:85-146
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LMO4_MOUSE	23-57 87-122	4	C:23-57 X:23-57 C:87-122 X:87-122

Biological Unit 1 (2, 4)

	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	2	- X:21-83 - X:85-146
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LMO4_MOUSE	23-57 87-122	2	- X:23-57 - X:87-122

Biological Unit 2 (2, 4)

	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	2	C:21-83 - C:85-146 -
2	LIM_DOMAIN_1	PS00478	LIM zinc-binding domain signature.	LMO4_MOUSE	23-57 87-122	2	C:23-57 - C:87-122 -

(no "Exon" information available for 2DFY)

Asymmetric Unit

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 C from PDB  Type:PROTEIN  Length:158
 aligned with LMO4_MOUSE | P61969 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:158
                                                                                                                                                                       160    161 165     
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158 |     162  |     
           LMO4_MOUSE    19 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSCCQAQLGDIGTSCYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSLQSNPLLP------DQKVC-----   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dfyC01 C:19-82,C:314-327 Cysteine Rich Protein                 2dfyC02 C:83-313 Cysteine Rich Protein                                          2dfyC01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee..eeehhhhh.......hhhhhh.eeeee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee.hhh.........ee....ee.........eee.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --LIM_DOMAIN_2  PDB: C:21-83 UniProt: 21-83                      -LIM_DOMAIN_2  PDB: C:85-146 UniProt: 85-147                    ----------------------------- PROSITE (1)
                PROSITE (2) ----LIM_DOMAIN_1  PDB: C:23-57         -----------------------------LIM_DOMAIN_1  PDB: C:87-122         ------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dfy C  19 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALIGGDVMVVGEPTLMGGEFGDEDERLITRLEN 327
                                    28        38        48        58        68        78        88        98       108       118       128       138       299       309       319        
                                                                                                                                                         146|                             
                                                                                                                                                          298

Chain X from PDB  Type:PROTEIN  Length:158
 aligned with LMO4_MOUSE | P61969 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:158
                                                                                                                                                                       160    161 165     
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158 |     162  |     
           LMO4_MOUSE    19 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSCCQAQLGDIGTSCYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSLQSNPLLP------DQKVC-----   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dfyX01 X:19-82,X:314-327 Cysteine Rich Protein                 2dfyX02 X:83-313 Cysteine Rich Protein                                          2dfyX01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee..eeehhhhh.......hhhhhh.eeeee..eeehhhhhhhhhh..ee......ee....eeeee..eeee.hhh.............eeeee..eeee.hhh.........ee....ee.........eee.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --LIM_DOMAIN_2  PDB: X:21-83 UniProt: 21-83                      -LIM_DOMAIN_2  PDB: X:85-146 UniProt: 85-147                    ----------------------------- PROSITE (1)
                PROSITE (2) ----LIM_DOMAIN_1  PDB: X:23-57         -----------------------------LIM_DOMAIN_1  PDB: X:87-122         ------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dfy X  19 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALIGGDVMVVGEPTLMGGEFGDEDERLITRLEN 327
                                    28        38        48        58        68        78        88        98       108       118       128       138       299       309       319        
                                                                                                                                                         146|                             
                                                                                                                                                          298

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 2DFY)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Cysteine Rich Protein (18)

Homologous Superfamily: Cysteine Rich Protein (18)

House mouse (Mus musculus) (4)

1a	2dfyC01	C:19-82,C:314-327
1b	2dfyX01	X:19-82,X:314-327
1c	2dfyC02	C:83-313
1d	2dfyX02	X:83-313

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

Asymmetric Unit(hide GO term definitions)

Chain C,X (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.

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	LMO4_MOUSE \| P61969	:	1m3v 1rut 2mbv

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