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(-) Description

Title :  NMR SOLUTION STRUCTURE OF A LDB1-LID:LHX3-LIM COMPLEX
 
Authors :  C. Lee, A. L. Nancarrow, J. P. Mackay, J. M. Matthews
Date :  03 Aug 07  (Deposition) - 17 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Intramolecular (Fusion) Protein-Protein Complex, Protein Binding/Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bhati, C. Lee, A. L. Nancarrow, M. Lee, V. J. Craig, I. Bach, J. M. Guss, J. P. Mackay, J. M. Matthews
Implementing The Lim Code: The Structural Basis For Cell Type-Specific Assembly Of Lim-Homeodomain Complexes
Embo J. V. 27 2018 2008
PubMed-ID: 18583962  |  Reference-DOI: 10.1038/EMBOJ.2008.123
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIM DOMAIN-BINDING PROTEIN 1, LIM/HOMEOBOX PROTEIN LHX3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System VectorPGEX-2T
    Expression System Vector TypeVECTOR
    FragmentFUSION OF LDB1 RESIDUES 295-340 AND LHX3 LIM ZINC-BINDING DOMAINS 1 AND 2
    GeneLDB1, NLI, LHX3, LIM-3, LIM3, PLIM
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    SynonymNUCLEAR LIM INTERACTOR, LIM HOMEOBOX PROTEIN 3, HOMEOBOX PROTEIN LIM-3, HOMEOBOX PROTEIN P-LIM

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

NMR Structure (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:63 , GLY A:65 , CYS A:66 , ILE A:70 , HIS A:84BINDING SITE FOR RESIDUE ZN A 183
2AC2SOFTWARECYS A:90 , ASP A:92 , TYR A:109 , CYS A:110 , ASP A:113BINDING SITE FOR RESIDUE ZN A 184
3AC3SOFTWARECYS A:122 , ALA A:124 , CYS A:125 , LEU A:127 , TYR A:143 , HIS A:144BINDING SITE FOR RESIDUE ZN A 185
4AC4SOFTWAREALA A:149 , CYS A:150 , CYS A:153 , ARG A:155BINDING SITE FOR RESIDUE ZN A 186

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIM_DOMAIN_2PS50023 LIM domain profile.LHX3_MOUSE32-91
92-154
  2A:61-120
A:121-182
2LIM_DOMAIN_1PS00478 LIM zinc-binding domain signature.LHX3_MOUSE34-68
93-128
  2A:63-97
A:122-157

(-) Exons   (0, 0)

(no "Exon" information available for 2JTN)

(-) 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
(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:182
 aligned with A2ALD9_MOUSE | A2ALD9 from UniProtKB/TrEMBL  Length:400

    Alignment length:182
                                         1          13               14                                                                                                                                           
                                     -   |     7     |   -         -  |     21        31        41        51        61        71        81        91       101       111       121       131       141       151  
         A2ALD9_MOUSE     - -------------MLLEAELDCHRER----------------PGAPGASALCTFSRTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ 153
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------LIM-2jtnA01 A:122-181                                       - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------LIM-2jtnA02 A:122-181                                       - Pfam domains (2)
         Sec.struct. author .......ee...................eeee.........................................eeeee..eee..................eee..eeehhhhhhhh...................ee..ee...................eeee.....eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jtn A   1 SSQVPDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  

Chain A from PDB  Type:PROTEIN  Length:182
 aligned with LHX3_MOUSE | P50481 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:182
                                         1          13               14                                                                                                                                           
                                     -   |     7     |   -         -  |     21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           LHX3_MOUSE     - -------------MLLEAELDCHRER----------------PGAPGASALCTFSRTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ 153
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------LIM-2jtnA01 A:122-181                                       - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------LIM-2jtnA02 A:122-181                                       - Pfam domains (2)
         Sec.struct. author .......ee...................eeee.........................................eeeee..eee..................eee..eeehhhhhhhh...................ee..ee...................eeee.....eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------LIM_DOMAIN_2  PDB: A:61-120 UniProt: 32-91                  LIM_DOMAIN_2  PDB: A:121-182 UniProt: 92-154                   PROSITE (1)
                PROSITE (2) --------------------------------------------------------------LIM_DOMAIN_1  PDB: A:63-97         ------------------------LIM_DOMAIN_1  PDB: A:122-157        ------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jtn A   1 SSQVPDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  

   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Family: LIM (23)
1aLIM-2jtnA01A:122-181
1bLIM-2jtnA02A:122-181

(-) Gene Ontology  (61, 72)

NMR Structure(hide GO term definitions)
Chain A   (A2ALD9_MOUSE | A2ALD9)
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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    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.

Chain A   (LHX3_MOUSE | P50481)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0001076    transcription factor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II 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.
    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:0009953    dorsal/ventral pattern formation    The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0021526    medial motor column neuron differentiation    The process in which differentiating motor neurons in the neural tube acquire the specialized structural and/or functional features of medial motor column neurons. Medial motor column neurons are generated at all rostrocaudal levels and send axons to the axial muscles (medial group) and to the body wall muscles (lateral group). Differentiation includes the processes involved in commitment of a cell to a specific fate.
    GO:0008045    motor neuron axon guidance    The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0021983    pituitary gland development    The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases 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: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:0021520    spinal cord motor neuron cell fate specification    The process in which a cell becomes capable of differentiating autonomously into a motor neuron in an environment that is neutral with respect to the developmental pathway.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0021521    ventral spinal cord interneuron specification    The process in which a cell becomes capable of differentiating autonomously into a ventral spinal cord interneuron in an environment that is neutral with respect to the developmental pathway.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LDB1_MOUSE | P706621j2o 1m3v 1rut 2l6y 2l6z 2lxd 4jcj
        LHX3_MOUSE | P504812rgt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2JTN)