4C6S - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE TIR DOMAIN FROM THE ARABIDOPSIS THALIANA DISEASE RESISTANCE PROTEIN RRS1

Authors :   L. Wan, S. J. Williams, K. H. Sohn, M. Bernoux, Y. Ma, C. Segonzac, T. Ve, P D. J. Ericsson, S. B. Saucet, X. Zhang, J. Parker, P. N. Dodds, J. D. G. Jo B. Kobe

Date :   19 Sep 13 (Deposition) - 28 May 14 (Release) - 28 May 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Immune System, Plant Tir Domain, Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Williams, K. H. Sohn, L. Wan, M. Bernoux, P. F. Sarris, C. Segonzac T. Ve, Y. Ma, S. B. Saucet, D. J. Ericsson, L. W. Casey, T. Lonhienne, D. J. Winzor, X. Zhang, A. Coerdt, J. E. Parker, P. N. Dodds, B. Kobe, J. D. G. Jones
Structural Basis For Assembly And Function Of A Heterodimeric Plant Immune Receptor.
Science V. 344 299 2014
PubMed-ID: 24744375 | Reference-DOI: 10.1126/SCIENCE.1247357

Molecule 1 - PROBABLE WRKY TRANSCRIPTION FACTOR 52
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA
	Expression System Vector Type	:	PLASMID
	Fragment	:	TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN, RESIDUES 7-153
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	DISEASE RESISTANCE PROTEIN RRS1, DISEASE RESISTANCE PROTEIN SLH1, PROTEIN SENSITIVE TO LOW HUMIDITY 1, RESISTANCE TO RALSTONIA SOLANACEARUM 1 PROTEIN, WRKY DNA-BINDING PROTEIN 52

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NA	2	Ligand/Ion	SODIUM ION
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:21 , TYR A:101 , ASP A:103 , SER A:125 , ARG A:126 , CYS A:129 , ASP A:131 , HOH A:2045	BINDING SITE FOR RESIDUE GOL A1150
2	AC2	SOFTWARE	PHE A:147 , VAL A:149	BINDING SITE FOR RESIDUE GOL A1151
3	AC3	SOFTWARE	VAL A:19 , PRO A:68 , GLY A:69 , ASN A:70 , TYR A:101 , HOH A:2024 , HOH A:2035	BINDING SITE FOR RESIDUE SO4 A1152
4	AC4	SOFTWARE	ARG A:107 , ARG A:126 , LYS A:127	BINDING SITE FOR RESIDUE SO4 A1153
5	AC5	SOFTWARE	HIS A:123 , GLN A:124 , ARG A:126 , NA A:1155	BINDING SITE FOR RESIDUE SO4 A1154
6	AC6	SOFTWARE	HIS A:123 , GLU A:137 , SO4 A:1154	BINDING SITE FOR RESIDUE NA A1155
7	AC7	SOFTWARE	GLU A:29 , GLN A:109 , HOH A:2010	BINDING SITE FOR RESIDUE NA A1156

(no "SS Bond" information available for 4C6S)

(no "Cis Peptide Bond" information available for 4C6S)

(no "SAP(SNP)/Variant" information available for 4C6S)

(no "PROSITE Motif" information available for 4C6S)

(no "Exon" information available for 4C6S)

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 A from PDB  Type:PROTEIN  Length:142
 aligned with WR52C_ARATH | P0DKH5 from UniProtKB/Swiss-Prot  Length:1288

    Alignment length:142
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147  
          WR52C_ARATH     8 EEFVCISCVEEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQAKIEKAGVSVMVLPGNCDPSEVWLDKFAKVLECQRNNKDQAVVSVLYGDSLLRDQWLSELDFRGLSRIHQSRKECSDSILVEEIVRDVYETHFYV 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c6s A   8 EEFVCISCVEEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQAKIEKAGVSVMVLPGNCDPSEVWLDKFAKVLECQRNNKDQAVVSVLYGDSLLRDQWLSELDFRGLSRIHQSRKECSDSILVEEIVRDVYETHFYV 149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147

Chain A from PDB  Type:PROTEIN  Length:142
 aligned with WR52N_ARATH | E1B328 from UniProtKB/Swiss-Prot  Length:1378

    Alignment length:142
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147  
          WR52N_ARATH     8 EEFVCISCVEEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQAKIEKAGVSVMVLPGNCDPSEVWLDKFAKVLECQRNNKDQAVVSVLYGDSLLRDQWLSELDFRGLSRIHQSRKECSDSILVEEIVRDVYETHFYV 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c6s A   8 EEFVCISCVEEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQAKIEKAGVSVMVLPGNCDPSEVWLDKFAKVLECQRNNKDQAVVSVLYGDSLLRDQWLSELDFRGLSRIHQSRKECSDSILVEEIVRDVYETHFYV 149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147

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 4C6S)

(no "CATH Domain" information available for 4C6S)

(no "Pfam Domain" information available for 4C6S)

Asymmetric Unit(hide GO term definitions)

Chain A (WR52N_ARATH | E1B328)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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 (WR52C_ARATH | P0DKH5)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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4c6r	CRYSTAL STRUCTURE OF THE TIR DOMAIN FROM THE ARABIDOPSIS THALIANA DISEASE RESISTANCE PROTEIN RPS4
4c6t	CRYSTAL STRUCTURE OF THE RPS4 AND RRS1 TIR DOMAIN HETERODIMER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (12, 24)

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