1FJL | PDE025 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE

Authors :   D. S. Wilson, B. Guenther, C. Desplan, J. Kuriyan

Date :   17 Dec 95 (Deposition) - 20 Jun 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dna-Binding Protein, Dna, Paired Box, Transcription Regulation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. S. Wilson, B. Guenther, C. Desplan, J. Kuriyan
High Resolution Crystal Structure Of A Paired (Pax) Class Cooperative Homeodomain Dimer On Dna.
Cell(Cambridge, Mass. ) V. 82 709 1995
PubMed-ID: 7671301 | Reference-DOI: 10.1016/0092-8674(95)90468-9
(for further references see the PDB file header)

Molecule 1 - PAIRED PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	HOMEODOMAIN
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	PRD, PAIRED PROTEIN

*Molecule 2 - DNA (5'- D(APAPTPAPAPTPCPTPGPAPTPTPAPC)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(TPGPTPAPAPTPCPAPGPAPTPTPAPT)-3')*
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 4 - DNA (5'- D(TPGPTPAPAPTPCPTPGPAPTPTPAPC)-3')*
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1FJL)

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

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

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRD_DROME_002 *	F	220	I	PRD_DROME	---	---	A/B/C	F	8	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRD_DROME_002 *	F	220	I	PRD_DROME	---	---	A/B	F	8	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRD_DROME_002 *	F	220	I	PRD_DROME	---	---	C	F	8	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	PRD_DROME	246-269	3	A:34-57 B:34-57 C:34-57

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	PRD_DROME	246-269	2	A:34-57 B:34-57 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	PRD_DROME	246-269	2	- - C:34-57

(no "Exon" information available for 1FJL)

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:65
 aligned with PRD_DROME | P06601 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:65
                                   221       231       241       251       261       271     
            PRD_DROME   212 KQRRCRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFSNRRARLRKQHTSVS 276
               SCOP domains d1fjla_ A: Paired protein                                         SCOP domains
               CATH domains 1fjlA00 A:0-64 Homeodomain-like                                   CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------I-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------HOMEOBOX_1  PDB: A:34-57------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 1fjl A   0 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTSVS  64
                                     9        19        29        39        49        59

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with PRD_DROME | P06601 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:58
                                   222       232       242       252       262        
            PRD_DROME   213 QRRCRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFSNRRARLRK 270
               SCOP domains d1fjlb_ B: Paired protein                                  SCOP domains
               CATH domains 1fjlB00 B:1-58 Homeodomain-like                            CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------I-------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------HOMEOBOX_1  PDB: B:34-57- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1fjl B   1 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK  58
                                    10        20        30        40        50

Chain C from PDB  Type:PROTEIN  Length:59
 aligned with PRD_DROME | P06601 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:59
                                   221       231       241       251       261         
            PRD_DROME   212 KQRRCRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFSNRRARLRK 270
               SCOP domains d1fjlc_ C: Paired protein                                   SCOP domains
               CATH domains 1fjlC00 C:0-58 Homeodomain-like                             CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------I-------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------HOMEOBOX_1  PDB: C:34-57- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 1fjl C   0 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK  58
                                     9        19        29        39        49

Chain D from PDB  Type:DNA  Length:16
                                                
                 1fjl D   1 ATATAATCTAGATTAC  14
                                     8

Chain E from PDB  Type:DNA  Length:16
                                                
                 1fjl E   1 TAGTAATCATGATTAT  14
                                     8

Chain F from PDB  Type:DNA  Length:16
                                                
                 1fjl F   1 TAGTAATCTAGATTAC  14
                                     8

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(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

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

Superfamily: Homeodomain-like (373)

Family: Homeodomain (93)

Protein domain: Paired protein (1)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (1)

1a	d1fjla_	A:
1b	d1fjlb_	B:
1c	d1fjlc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

Fruit fly (Drosophila melanogaster) (14)

1a	1fjlC00	C:0-58
1b	1fjlB00	B:1-58
1c	1fjlA00	A:0-64

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PRD_DROME | P06601)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by 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:0003705	transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
biological process
	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:0007366	periodic partitioning by pair rule gene	Allocation of cells to parasegments in the embryo, through the action of overlapping series of pair rule gene activities.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	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 Unit
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Biological Units
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