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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CSL (LAG-1) BOUND TO DNA WITH LIN-12 RAM PEPTIDE, P212121

Authors :   J. J. Wilson, R. A. Kovall

Date :   21 Dec 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Protein-Dna Complex, Signaling, Transcription, Notch, Dna- Binding, Ank Repeat, Developmental Protein, Differentiation, Egf-Like Domain, Glycoprotein, Membrane, Transmembrane, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Friedmann, J. J. Wilson, R. A. Kovall
Ram-Induced Allostery Facilitates Assembly Of A Notch Pathway Active Transcription Complex.
J. Biol. Chem. V. 283 14781 2008
PubMed-ID: 18381292 | Reference-DOI: 10.1074/JBC.M709501200
(for further references see the PDB file header)

Molecule 1 - LIN-12 AND GLP-1 PHENOTYPE PROTEIN 1, ISOFORM A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE DOMAIN
	Gene	:	LAG-1
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Synonym	:	DNA-BINDING PROTEIN LAG-1, LAG-1 PROTEIN

Molecule 2 - PROTEIN LIN-12
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RAM PEPTIDE
	Gene	:	LIN-12
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Synonym	:	ABNORMAL CELL LINEAGE PROTEIN 12

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

*Molecule 4 - DNA (5'- D(DAPDAPDTPDCPDTPDTPDTPDCPDCPDCPDAPDCPDAPDGP DT)-3')**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 10)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:220 , CYS A:241 , TYR A:243 , TRP A:422 , ALA A:424 , HOH A:757 , HOH A:760	BINDING SITE FOR RESIDUE EDO A 1
02	AC2	SOFTWARE	THR A:629 , ASN A:630 , ARG A:631	BINDING SITE FOR RESIDUE EDO A 2
03	AC3	SOFTWARE	GLU A:545 , ARG A:547 , SER A:651 , GLY A:653	BINDING SITE FOR RESIDUE EDO A 3
04	AC4	SOFTWARE	GLN A:361 , LYS A:543 , ALA A:544 , GLU A:545	BINDING SITE FOR RESIDUE EDO A 4
05	AC5	SOFTWARE	GLN A:300 , GLN A:301 , ALA A:326 , ALA A:327 , LYS A:328 , THR A:329	BINDING SITE FOR RESIDUE EDO A 5
06	AC6	SOFTWARE	THR A:462 , GLY A:463 , ILE A:464 , ALA D:942 , SER D:943	BINDING SITE FOR RESIDUE EDO D 6
07	AC7	SOFTWARE	DT C:6	BINDING SITE FOR RESIDUE EDO C 16
08	AC8	SOFTWARE	TYR A:289 , PHE A:348	BINDING SITE FOR RESIDUE EDO A 8
09	AC9	SOFTWARE	LEU A:207 , MET A:627 , PHE A:628 , PRO A:639	BINDING SITE FOR RESIDUE EDO A 9
10	BC1	SOFTWARE	ARG A:445 , PHE A:448 , GLU A:580 , ARG A:604 , HOH A:699	BINDING SITE FOR RESIDUE EDO A 10

(no "SS Bond" information available for 3BRD)

Asymmetric/Biological Unit

No.	Residues
1	Cys A:237	-	Pro A:238
2	Ser A:560	-	Pro A:561

(no "SAP(SNP)/Variant" information available for 3BRD)

(no "PROSITE Motif" information available for 3BRD)

(no "Exon" information available for 3BRD)

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 A from PDB  Type:PROTEIN  Length:427
 aligned with Q8MXE7_CAEEL | Q8MXE7 from UniProtKB/TrEMBL  Length:671

    Alignment length:467
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       
         Q8MXE7_CAEEL   193 VQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKLKKDRVAQLYKTLKASAQKDAAIENDPIHEQQATELVAYIGIGSDTSERQQLDFSTGKVRHPGDQRQDPNIYDYCAAKTLYISDSDKRKYFDLNAQFFYGCGMEIGGFVSQRIKVISKPSKKKQSMKNTDCKYLCIASGTKVALFNRLRSQTVSTRYLHVEGNAFHASSTKWGAFTIHLFDDERGLQETDNFAVRDGFVYYGSVVKLVDSVTGIALPRLRIRKVDKQQVILDASCSEEPVSQLHKCAFQMIDNELVYLCLSHDKIIQHQATAINEHRHQINDGAAWTIISTDKAEYRFFEAMGQVANPISPCPVVGSLEVDGHGEASRVELHGRDFKPNLKVWFGATPVETTFRSEESLHCSIPPVSQVRNEQTHWMFTNRTTGDVEVPISLVRDDGVVYSSGLTFSYKSL 659
               SCOP domains d3brda2 A:195-380 DNA-binding protein LAG-1 (CSL)                                                                                                                                         d3brda3 A:381-541 DNA-binding protein LAG-1 (CSL)                                                                                                                d3brda1 A:542-661 DNA-binding protein LAG-1 (CSL)                                                                        SCOP domains
               CATH domains 3brdA01 A:195-373,A:541-562 Lin-12 and glp-1 transcriptional regulato                 r; domain 1                                                                                       3brdA02 A:379-540  [code=2.80.10.50, no name defined]                                                                                                             3brdA01               3brdA03 A:563-661 Immunoglobulins                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhheeeeeeee.eee..............eeeee.hhhhhhhhhhhhh....-----------------.....eeeeee........ee...--------------..eeeeee.............ee..eeeeee....eeeeee...eeee.......-----.hhhhhh.....eeeeee....hhhhheeeeee..eeeee......eeeeee..----....eeeee........eeeeee.........eeeeeee..eee...hhhhh.....eeeeeee.....eeeeee..eeeeee.eeee..eee.hhhhheeeeeeeeeeeeeee.............eeeeeeee.hhhh.eeeeeee.....eeeee..eee.eeeee..eeeee..hhhhhh...hhhhhh.......eeeeeeee...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brd A 195 VQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKLKKDRVAQLYKTL-----------------QQATELVAYIGIGSDTSERQQLDF--------------PNIYDYCAAKTLYISDSDKRKYFDLNAQFFYGCGMEIGGFVSQRIKVISKPSKKK-----TDCKYLCIASGTKVALFNRLRSQTVSTRYLHVEGNAFHASSTKWGAFTIHLFDD----QETDNFAVRDGFVYYGSVVKLVDSVTGIALPRLRIRKVDKQQVILDASCSEEPVSQLHKCAFQMIDNELVYLCLSHDKIIQHQATAINEHRHQINDGAAWTIISTDKAEYRFFEAMGQVANPISPCPVVGSLEVDGHGEASRVELHGRDFKPNLKVWFGATPVETTFRSEESLHCSIPPVSQVRNEQTHWMFTNRTTGDVEVPISLVRDDGVVYSSGLTFSYKSL 661
                                   204       214       224       234       244       254        |-         -      |284       294       304         -    |  324       334       344       354       364        |-    |  384       394       404       414       424       | -  |    444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       
                                                                                              263               281                    304            319                                                   373   379                                                  432  437

Chain B from PDB  Type:DNA  Length:15
                                               
                 3brd B   1 TTACTGTGGGAAAGA  15
                                    10

Chain C from PDB  Type:DNA  Length:15
                                               
                 3brd C   1 AATCTTTCCCACAGT  15
                                    10

Chain D from PDB  Type:PROTEIN  Length:15
 aligned with LIN12_CAEEL | P14585 from UniProtKB/Swiss-Prot  Length:1429

    Alignment length:15
                                   946     
          LIN12_CAEEL   937 RRMINASVWMPPMEN 951
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 3brd D 937 RRMINASVWMPPMEN 951
                                   946

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 "Pfam Domain" information available for 3BRD)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q8MXE7_CAEEL | Q8MXE7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005112	Notch binding	Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	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:0000982	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
	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:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0001708	cell fate specification	The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
	GO:0043054	dauer exit	Exit from the facultative diapause of the dauer (enduring) larval stage of nematode development.
	GO:0042078	germ-line stem cell division	The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes.
	GO:0002119	nematode larval development	The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
	GO:0018991	oviposition	The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
	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:0040026	positive regulation of vulval development	Any process that activates or increases the frequency, rate or extent of development of the vulva. Vulval development is the process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.
	GO:0042659	regulation of cell fate specification	Any process that mediates the adoption of a specific fate by a cell.
	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 D (LIN12_CAEEL | P14585)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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:0001708	cell fate specification	The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
	GO:0045168	cell-cell signaling involved in cell fate commitment	Signaling at long or short range between cells that results in the commitment of a cell to a certain fate.
	GO:0043054	dauer exit	Exit from the facultative diapause of the dauer (enduring) larval stage of nematode development.
	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:0002119	nematode larval development	The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
	GO:0018991	oviposition	The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
	GO:0040025	vulval development	The process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Cys A:237 - Pro A:238	[ RasMol ]
		Ser A:560 - Pro A:561	[ RasMol ]

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	LIN12_CAEEL \| P14585	:	2fo1 3brf
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