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Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE NAC DOMAIN OF ANAC019 IN COMPLEX WITH DNA, GOLD DERIVATIVE

Authors :   D. Welner, L. Lo Leggio

Date :   14 Jul 11 (Deposition) - 11 Apr 12 (Release) - 13 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.25

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

Keywords :   Mostly Beta-Sheet, Transcription Factor, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Welner, S. Lindemose, J. G. Grossmann, N. E. Mollegaard, A. N. Olsen, C. Helgstrand, K. Skriver, L. Lo Leggio
Dna Binding By The Plant-Specific Nac Transcription Factors In Crystal And Solution: A Firm Link To Wrky And Gcm Transcription Factors.
Biochem. J. V. 444 395 2012
PubMed-ID: 22455904 | Reference-DOI: 10.1042/BJ20111742

Molecule 1 - NAC DOMAIN-CONTAINING PROTEIN 19
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	NAC DOMAIN (UNP RESIDUES 1-168)
	Gene	:	NAC019, ANAC, AT1G52890, F14G24.16
	Organism Common	:	MOUSE-EAR CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	ANAC019, ABSCICIC-ACID-RESPONSIVE NAC, ANAC

Molecule 2 - OLIGONUCLEOTIDE FORWARD
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - OLIGONUCLEOTIDE REVERSE
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 9)

No.	Name	Count	Type	Full Name
1	AU	9	Ligand/Ion	GOLD ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:33 , AU A:171 , ASN C:61	BINDING SITE FOR RESIDUE AU A 169
2	AC2	SOFTWARE	AU A:170 , CYS C:33 , VAL C:111	BINDING SITE FOR RESIDUE AU C 169
3	AC3	SOFTWARE	ASN A:61 , CYS C:33 , AU C:169	BINDING SITE FOR RESIDUE AU A 170
4	AC4	SOFTWARE	CYS A:33 , ALA A:36 , ALA A:37	BINDING SITE FOR RESIDUE AU C 170
5	AC5	SOFTWARE	CYS A:33 , VAL A:111 , AU A:169	BINDING SITE FOR RESIDUE AU A 171
6	AC6	SOFTWARE	TYR C:52 , MET C:134 , GLU C:136 , CYS C:157	BINDING SITE FOR RESIDUE AU C 171
7	AC7	SOFTWARE	VAL A:29 , CYS A:33 , ARG A:34 , ASP C:55	BINDING SITE FOR RESIDUE AU C 172
8	AC8	SOFTWARE	CYS D:33 , VAL D:111	BINDING SITE FOR RESIDUE AU D 169
9	AC9	SOFTWARE	CYS B:33 , VAL B:111	BINDING SITE FOR RESIDUE AU B 169

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:124	-	Pro A:125
2	Ala B:124	-	Pro B:125
3	Ala C:124	-	Pro C:125
4	Ala D:124	-	Pro D:125

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NAC	PS51005	NAC domain profile.	NAC19_ARATH	14-162	4	A:14-162 B:14-162 C:14-162 D:14-162

(no "Exon" information available for 3SWM)

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:141
 aligned with NAC19_ARATH | Q9C932 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:156
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      
          NAC19_ARATH     8 PLTQLSLPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRDRKYPNGSRPNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPSRRNGSTKLDDWVLCRIYKKQ 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....eee..hhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhh.....eeeeeee...-------...ee..eeeeeeeeeeeeee..eeeeeeeeeeeee......eeeeeeeeeeee....--------..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------NAC  PDB: A:14-162 UniProt: 14-162                                                                                                                   - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3swm A   8 PLTQLSLPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRDR-------PNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPS--------DDWVLCRIYKKQ 163
                                    17        27        37        47        57        67        77|       87        97       107       117       127       137     |   -    |  157      
                                                                                                 78      86                                                      143      152

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with NAC19_ARATH | Q9C932 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:156
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      
          NAC19_ARATH     8 PLTQLSLPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRDRKYPNGSRPNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPSRRNGSTKLDDWVLCRIYKKQ 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhh.....eeeeeee..--------...ee..eeeeeeeeeeeeee..eeeeeeeeeeeee......eeeeeeeeeeee....--------..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------NAC  PDB: B:14-162 UniProt: 14-162                                                                                                                   - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3swm B   8 PLTQLSLPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRD--------PNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPS--------DDWVLCRIYKKQ 163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137     |   -    |  157      
                                                                                                77       86                                                      143      152

Chain C from PDB  Type:PROTEIN  Length:135
 aligned with NAC19_ARATH | Q9C932 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:150
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163
          NAC19_ARATH    14 LPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRDRKYPNGSRPNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPSRRNGSTKLDDWVLCRIYKKQ 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhh.....eeeeeee...-------...ee..eeeeeeeeeeeeee..eeeeeeeeeeeee......eeeeeeeeeeee....--------..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE NAC  PDB: C:14-162 UniProt: 14-162                                                                                                                   - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3swm C  14 LPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRDR-------PNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPS--------DDWVLCRIYKKQ 163
                                    23        33        43        53        63        73    |    -  |     93       103       113       123       133       143       153       163
                                                                                           78      86                                                      143      152

Chain D from PDB  Type:PROTEIN  Length:140
 aligned with NAC19_ARATH | Q9C932 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:156
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      
          NAC19_ARATH     8 PLTQLSLPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRDRKYPNGSRPNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPSRRNGSTKLDDWVLCRIYKKQ 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....ee...hhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhh.....eeeeeee..--------...ee..eeeeeeeeeeeeee..eeeeeeeeeeeee......eeeeeeeeeeee....--------..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------NAC  PDB: D:14-162 UniProt: 14-162                                                                                                                   - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3swm D   8 PLTQLSLPPGFRFYPTDEELMVQYLCRKAAGYDFSLQLIAEIDLYKFDPWVLPNKALFGEKEWYFFSPRD--------PNRVAGSGYWKATGTDKIISTEGQRVGIKKALVFYIGKAPKGTKTNWIMHEYRLIEPS--------DDWVLCRIYKKQ 163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137     |   -    |  157      
                                                                                                77       86                                                      143      152

Chain E from PDB  Type:DNA  Length:26
                                                          
                 3swm E   1 GTCTTGCGTGTTGGAACACGCAACAG  26
                                    10        20

Chain F from PDB  Type:DNA  Length:26
                                                          
                 3swm F   1 CCTGTTGCGTGTTCCAACACGCAAGA  26
                                    10        20

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 3SWM)

(no "CATH Domain" information available for 3SWM)

(no "Pfam Domain" information available for 3SWM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (NAC19_ARATH | Q9C932)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009414	response to water deprivation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:124 - Pro A:125	[ RasMol ]
		Ala B:124 - Pro B:125	[ RasMol ]
		Ala C:124 - Pro C:125	[ RasMol ]
		Ala D:124 - Pro D:125	[ RasMol ]

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	NAC19_ARATH \| Q9C932	:	1ut4 1ut7 3swp 4dul

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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Gene Ontology (7, 7)

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