1RUT - JenaLib

Asymmetric/Biological 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 X from PDB  Type:PROTEIN  Length:157
 aligned with LDB1_MOUSE | P70662 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:361
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362 
           LDB1_MOUSE     3 VGCACPGCSSKSFKLYSPKEPPNGNAFPPFHPGTMLDRDVGPTPMYPPTYLEPGIGRHTPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPKRYTIGRTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQVCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGLSNSTLNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPARQQPSKRRKRKMSGGSTMSSGGGNTNNSNSKKKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDERLITRLEN 363
               SCOP domains d1rutx1 X                       :19-48                                           d1r            utx2 X:     49-82 LIM only 4                          (Lmo4) d1r utx3 X:8                                    3-113                                                          -d1                    rutx4 X:114-146                       -------------------------------- SCOP domains
               CATH domains 1rutX01 X                       :19-82                            ,X:314-327 Cystein            e Rich      Protein                                          1ru tX02 X:8                                    3-313 Cystei                                        ne Ric   h  Pr                    otein                                                   1rutX01        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........-----------------------......----------------------------eeeee..eeehhhhh...------------....hhh-----hhh.eeeee..eeehh-------------------------hhhhhhhh..e-e......e------------------------------------e....eeeee..----------------------------------------eeehhh---hh-..--------------------...........eeeee..----eeee.hhh..---...-.--..ee....ee.........eee.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rut X  19 SWKRCAGCG-----------------------GKIADR----------------------------FLLYAMDSYWHSRCLKCS------------SCQAQLG-----DIGTSSYTKSGMILCR-------------------------NDYIRLFGNSG-ACSACGQS------------------------------------IPASELVMRAQG----------------------------------------NVYHLK---CF-TC--------------------STCRNRLVPGDRFHYING----SLFCEHDRPT---ALI-G--DVMVVGEPTLMGGEFGDEDERLITRLEN 327
                                    |-         -         -  |    | -         -         -      | 37        47   |     -      | 55  |     60        70   |     -         -        75        85 |      |-         -         -         -     |  98      |  -         -         -         -       108  |   |114|        -         - |     124        |-   |   140  |   | |-|  |   306       316       326 
                                   27                      28   33                           34               51           52    58    59             74                        75        85 |     93                                   94        105                                      106  111 112| ||                  116              133  134      143 144 | |  |                           
                                                                                                                                                                                            86                                                                                                       113 ||                                                       146 |  |                           
                                                                                                                                                                                                                                                                                                       114|                                                         211  |                           
                                                                                                                                                                                                                                                                                                        115                                                            300

Chain X from PDB  Type:PROTEIN  Length:157
 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 d1rutx1 X:19-48               d1rutx2 X:49-82 LIM only 4 (Lmo4) d1rutx3 X:83-113               d1rutx4 X:114-146                ------------------------------ SCOP domains
               CATH domains 1rutX01 X:19-82,X:314-327 Cysteine Rich Protein                 1rutX02 X:83-313 Cysteine Rich Protein                                          1rutX01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee..eeehhhhh.......hhhhhh.eeeee..eeehhhhhhhhhh..ee......ee....eeeee..eeehhhhh.............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
                 1rut X  19 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALI-GDVMVVGEPTLMGGEFGDEDERLITRLEN 327
                                    28        38        48        58        68        78        88        98       108       118       128       138       211|      309       319        
                                                                                                                                                         146 ||                           
                                                                                                                                                           211|                           
                                                                                                                                                            300

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 '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (LDB1_MOUSE | P70662)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030274	LIM domain binding	Interacting selectively and non-covalently with a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions.
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0043621	protein self-association	Interacting selectively and non-covalently with a domain within the same polypeptide.
	GO:0000989	transcription factor activity, transcription factor binding	Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0009948	anterior/posterior axis specification	The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0022607	cellular component assembly	The aggregation, arrangement and bonding together of a cellular component.
	GO:0021702	cerebellar Purkinje cell differentiation	The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Purkinje cell. Differentiation includes the processes involved in commitment of a neuroblast to a Purkinje cell fate. A Purkinje cell is an inhibitory GABAergic neuron found in the cerebellar cortex that projects to the deep cerebellar nuclei and brain stem.
	GO:0021549	cerebellum development	The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
	GO:0010669	epithelial structure maintenance	A tissue homeostatic process required for the maintenance of epithelial structure.
	GO:0001702	gastrulation with mouth forming second	A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
	GO:0001942	hair follicle development	The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
	GO:0060322	head development	The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body.
	GO:0043973	histone H3-K4 acetylation	The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 4 of the histone.
	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:0045647	negative regulation of erythrocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation.
	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:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0046985	positive regulation of hemoglobin biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
	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:0060319	primitive erythrocyte differentiation	Erythrocyte differentiation which occurs as part of the process of primitive hemopoiesis.
	GO:0032784	regulation of DNA-templated transcription, elongation	Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
	GO:0051893	regulation of focal adhesion assembly	Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
	GO:0043549	regulation of kinase activity	Any process that modulates 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:0035019	somatic stem cell population maintenance	Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
	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:0000972	transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
cellular component
	GO:0031252	cell leading edge	The area of a motile cell closest to the direction of movement.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	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 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.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (55, 62)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File