1FYM | PD0184 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A TAIL-TO-TAIL ORIENTATION

Authors :   O. Littlefield, H. C. M. Nelson

Date :   02 Oct 00 (Deposition) - 28 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (2x)
Biol. Unit 2: B,D  (2x)

Keywords :   Crystal-Packing Interface, Crystallization, Protein-Dna Interface, Protein-Protein Interface, Static Disorder, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Littlefield, H. C. Nelson
Crystal Packing Interaction That Blocks Crystallization Of A Site-Specific Dna Binding Protein-Dna Complex.
Proteins V. 45 219 2001
PubMed-ID: 11599025 | Reference-DOI: 10.1002/PROT.1142
(for further references see the PDB file header)

Molecule 1 - TAIL-TO-TAIL HSE
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE IS BASED ON AN IDEALIZED HSE SEQUENCE.
	Synthetic	:	YES

Molecule 2 - HEAT SHOCK TRANSCRIPTION PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHN280R
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN
	Mutation	:	YES
	Organism Scientific	:	KLUYVEROMYCES LACTIS
	Organism Taxid	:	28985
	Synonym	:	HEAT SHOCK TRANSCRIPTION FACTOR

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A		C
Biological Unit 2 (2x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1FYM)

(no "Site" information available for 1FYM)

(no "SS Bond" information available for 1FYM)

(no "Cis Peptide Bond" information available for 1FYM)

(no "SAP(SNP)/Variant" information available for 1FYM)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSF_DOMAIN	PS00434	HSF-type DNA-binding domain signature.	HSF_KLULA	236-260	2	A:236-260 B:236-260

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSF_DOMAIN	PS00434	HSF-type DNA-binding domain signature.	HSF_KLULA	236-260	2	A:236-260 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSF_DOMAIN	PS00434	HSF-type DNA-binding domain signature.	HSF_KLULA	236-260	2	- B:236-260

(no "Exon" information available for 1FYM)

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
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Chain A from PDB  Type:PROTEIN  Length:86
 aligned with HSF_KLULA | P22121 from UniProtKB/Swiss-Prot  Length:677

    Alignment length:165
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352     
            HSF_KLULA   193 ARPAFVNKLWSMVNDKSNEKFIHWSTSGESIVVPNRERFVQEVLPKYFKHSNFASFVRQLNMYGWHKVQDVKSGSMLSNNDSRWEFENENFKRGKEYLLENIVRQKSNTNILGGTTNAEVDIHILLNELETVKYNQLAIAEDLKRITKDNEMLWKENMMARERHQ 357
               SCOP domains d1fyma_ A: Heat-shock transcription factor                                                                                                                            SCOP domains
               CATH domains 1fymA00 A:193-284 'winged helix' repressor DNA binding domain                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...ee......eee.hhhhhhhhhhhhhh...hhhhhhhhhhhh.eee......------....eeeee.-------------------------------------------------------------------------... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------HSF_DOMAIN  PDB: A:236-26------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fym A 193 ARPAFVNKLWSMVNDKSNEKFIHWSTSGESIVVPNRERFVQEVLPKYFKHSNFASFVRQLNMYGWHKVQDVKS------NDSRWEFENE-------------------------------------------------------------------------RHA 284
                                   202       212       222       232       242       252       262  |    272        |-         -         -         -         -         -         -         -  |  
                                                                                                  265    272      281                                                                       282

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with HSF_KLULA | P22121 from UniProtKB/Swiss-Prot  Length:677

    Alignment length:88
                                   202       212       222       232       242       252       262       272        
            HSF_KLULA   193 ARPAFVNKLWSMVNDKSNEKFIHWSTSGESIVVPNRERFVQEVLPKYFKHSNFASFVRQLNMYGWHKVQDVKSGSMLSNNDSRWEFEN 280
               SCOP domains d1fymb_ B: Heat-shock transcription factor                                               SCOP domains
               CATH domains 1fymB00 B:193-280 'winged helix' repressor DNA binding domain                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...ee.....eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhh..ee...----------...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------HSF_DOMAIN  PDB: B:236-26-------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1fym B 193 ARPAFVNKLWSMVNDKSNEKFIHWSTSGESIVVPNRERFVQEVLPKYFKHSNFASFVRQLNMYGWHKVQD----------DSRWEFEN 280
                                   202       212       222       232       242       252       262         -|       
                                                                                               262        273

Chain C from PDB  Type:DNA  Length:12
                                            
                 1fym C   1 GGTTCTAGAACC  12
                                    10

Chain D from PDB  Type:DNA  Length:12
                                            
                 1fym D   1 GGTTCTAGAACC  12
                                    10

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: Heat-shock transcription factor (12)

Protein domain: Heat-shock transcription factor (11)

Milk yeast (Kluyveromyces lactis) [TaxId: 28985] (9)

1a	d1fyma_	A:
1b	d1fymb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

1a	1fymA00	A:193-284
1b	1fymB00	B:193-280

(no "Pfam Domain" information available for 1FYM)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HSF_KLULA | P22121)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0032007	negative regulation of TOR signaling	Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009408	response to heat	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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0030474	spindle pole body duplication	Construction of a new spindle pole body.
	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.

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	1fym
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	HSF_KLULA \| P22121
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UniProtKB/Swiss-Prot
	HSF_KLULA \| P22121	:	1fbq 1fbs 1fbu 1fyk 1fyl 2hts 3hsf 3hts

1fyk	SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA THAT IS TRANSLATIONALLY DISORDERED
1fyl	SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A HEAD-TO-HEAD ORIENTATION
2hts	HEAT SHOCK TRANSCRIPTION FACTOR DNA-BINDING DOMAIN
3hts	HEAT SHOCK TRANSCRIPTION FACTOR DNA-BINDING DOMAIN/DNA COMPLEX

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Ligands, Modified Residues, Ions (0, 0)

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