1B8I | PD0042 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX

Authors :   J. M. Passner, H. -D. Ryoo, L. Shen, R. S. Mann, A. K. Aggarwal

Date :   01 Feb 99 (Deposition) - 12 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Dna Binding, Homeodomain, Homeotic Proteins, Development, Specificity, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Passner, H. D. Ryoo, L. Shen, R. S. Mann, A. K. Aggarwal
Structure Of A Dna-Bound Ultrabithorax-Extradenticle Homeodomain Complex.
Nature V. 397 714 1999
PubMed-ID: 10067897 | Reference-DOI: 10.1038/17833
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(GPTPCPGPCPCPAPTPAPAPAPTPCPAPC)-3')**
	Chains	:	C
	Engineered	:	YES
	Fragment	:	UBX/EXD CONSENSUS BINDING SITE
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(APCPGPTPGPAPTPTPTPAPTPGPGPCPG)-3')**
	Chains	:	D
	Engineered	:	YES
	Fragment	:	UBX/EXD CONSENSUS BINDING SITE
	Synthetic	:	YES

Molecule 3 - PROTEIN (ULTRABITHORAX HOMEOTIC PROTEIN IV)
	Cellular Location	:	NUCLEUS
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET-3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	YPWM MOTIF AND HOMEODOMAIN
	Gene	:	UBX
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Other Details	:	IVA SPLICING ISOFORM OF THE UBX GENE WAS USED
	Synonym	:	ULTRABITHORAX

Molecule 4 - PROTEIN (HOMEOBOX PROTEIN EXTRADENTICLE)
	Cellular Location	:	NUCLEUS
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Taxid	:	562
	Fragment	:	HOMEODOMAIN
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	PBX PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1B8I)

(no "Site" information available for 1B8I)

(no "SS Bond" information available for 1B8I)

(no "Cis Peptide Bond" information available for 1B8I)

(no "SAP(SNP)/Variant" information available for 1B8I)

Asymmetric/Biological Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANTENNAPEDIA	PS00032	'Homeobox' antennapedia-type protein signature.	UBX_DROME	239-244	1	A:88-93
2	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	EXD_DROME	274-297	1	B:237-260
2	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	UBX_DROME	328-351	1	A:134-157
3	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	UBX_DROME	293-353	1	A:105-159

(no "Exon" information available for 1B8I)

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:62
 aligned with UBX_DROME | P83949 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:116
                                   248       258       268       278       288       298       308       318       328       338       348      
            UBX_DROME   239 FYPWMAIAGECPEDPTKSKIRSDLTQYGGISTDMGKRYSESLAGSLLPDWLGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 354
               SCOP domains d1b8ia                                                      _ A: Ultrabithorax (ubx) homeodomain                     SCOP domains
               CATH domains 1b8iA0                                                      0 A:88-160 Homeodomain-like                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......------------------------------------------------------.....hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ANTENN-----------------------------------------------------------------------------------HOMEOBOX_1              --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------HOMEOBOX_2  PDB: A:105-159 UniProt: 293-353                  - PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1b8i A  88 FYPWMA------------------------------------------------------RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI 160
                                 |   -         -         -         -         -         -|      114       124       134       144       154      
                                93                                                    105

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with EXD_DROME | P40427 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:58
                                   251       261       271       281       291        
            EXD_DROME   242 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKN 299
               SCOP domains d1b8ib_ B: Extradenticle (exd) homeodomain                 SCOP domains
               CATH domains 1b8iB00 B:205-262 Homeodomain-like                         CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..........hhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HOMEOBOX_1              -- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1b8i B 205 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKN 262
                                   214       224       234       244       254

Chain C from PDB  Type:DNA  Length:15
                                               
                 1b8i C   1 GTCGCCATAAATCAC  15
                                    10

Chain D from PDB  Type:DNA  Length:15
                                               
                 1b8i D  16 ACGTGATTTATGGCG  30
                                    25

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

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

Superfamily: Homeodomain-like (373)

Family: Homeodomain (93)

Protein domain: Extradenticle (exd) homeodomain (1)

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

d1b8ib_

Protein domain: Ultrabithorax (ubx) homeodomain (1)

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

d1b8ia_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

[unclassified] (65)

1a	1b8iB00	B:205-262
1b	1b8iA00	A:88-160

(no "Pfam Domain" information available for 1B8I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UBX_DROME | P83949)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
	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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	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:0061327	anterior Malpighian tubule development	The process whose specific outcome is the progression of the anterior Malpighian tubule over time, from its formation to the mature structure. The pair of anterior tubules arise from a dorsal region of the embryonic hindgut and projects forwards through the body cavity. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which connects with the posterior part of the gut.
	GO:0009952	anterior/posterior pattern specification	The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0001709	cell fate determination	A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
	GO:0035052	dorsal vessel aortic cell fate commitment	The commitment of dorsal vessel cardioblast cells to an aortic cell fate and their capacity to differentiate into aortic cells. An example of this process is found in Drosophila melanogaster.
	GO:0001706	endoderm formation	The formation of the endoderm during gastrulation.
	GO:0007482	haltere development	The process whose specific outcome is the progression of the haltere over time, from its formation to the mature structure. The haltere is the club-shaped 'balancers' found on each side of the metathorax among the true flies (Diptera). They are the much-modified hind wings.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0007480	imaginal disc-derived leg morphogenesis	The process in which the anatomical structures of a leg derived from an imaginal disc are generated and organized. A leg is a limb on which an animal walks and stands. An example of this is found in Drosophila melanogaster.
	GO:0007501	mesodermal cell fate specification	The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
	GO:0007494	midgut development	The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.
	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:0042694	muscle cell fate specification	The process in which a cell becomes capable of differentiating autonomously into a muscle cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
	GO:0060969	negative regulation of gene silencing	Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0007424	open tracheal system development	The process whose specific outcome is the progression of an open tracheal system over time, from its formation to the mature structure. An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.
	GO:0048636	positive regulation of muscle organ development	Any process that activates, maintains or increases the rate of muscle development.
	GO:0042659	regulation of cell fate specification	Any process that mediates the adoption of a specific fate by a cell.
	GO:0045570	regulation of imaginal disc growth	Any process that modulates the frequency, rate or extent of the growth of the imaginal disc.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007525	somatic muscle development	The process whose specific outcome is the progression of the somatic muscle over time, from its formation to the mature structure. Somatic muscles are striated muscle structures that connect to the exoskeleton or cuticle.
	GO:0010092	specification of animal organ identity	The regionalization process in which the identity of an animal organ primordium is specified. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
	GO:0007385	specification of segmental identity, abdomen	The specification of the characteristic structures of the abdominal segments following establishment of segment boundaries. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
	GO:0007384	specification of segmental identity, thorax	The specification of the characteristic structures of the thoracic segments following establishment of segment boundaries. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
	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.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain B (EXD_DROME | P40427)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0033613	activating transcription factor binding	Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
	GO:0035326	enhancer binding	Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	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.
	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.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0001654	eye development	The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
	GO:0007479	leg disc proximal/distal pattern formation	The establishment, maintenance and elaboration of the proximal/distal axis of the leg imaginal disc, a precursor to the adult leg.
	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:0007438	oenocyte development	The process whose specific outcome is the progression of the oenocyte over time, from its formation to the mature structure. The oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments.
	GO:0007422	peripheral nervous system development	The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
	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:0000060	protein import into nucleus, translocation	A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
	GO:0042659	regulation of cell fate specification	Any process that mediates the adoption of a specific fate by a cell.
	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:0007432	salivary gland boundary specification	Determination of where the salivary gland forms, the total number of salivary gland cells and how many cells are allocated to each of the specialised cell types within the salivary gland.
	GO:0007525	somatic muscle development	The process whose specific outcome is the progression of the somatic muscle over time, from its formation to the mature structure. Somatic muscles are striated muscle structures that connect to the exoskeleton or cuticle.
	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.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Asymmetric/Biological Unit
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	1b8i
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	UBX_DROME \| P83949
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	EXD_DROME \| P40427	:	2r5y 2r5z 4cyc 4uus
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(no "Related Entries Specified in the PDB File" available for 1B8I)

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SCOP Domains (2, 2)

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