2R5Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF SCR/EXD COMPLEX BOUND TO A CONSENSUS HOX-EXD SITE

Authors :   A. K. Aggarwal, J. M. Passner, R. Jain

Date :   04 Sep 07 (Deposition) - 05 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Homeodomain, Homeotic Proteins, Specificity, Developmental Protein, Dna-Binding, Homeobox, Nucleus, Transcription, Transcription Regulation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Joshi, J. M. Passner, R. Rohs, R. Jain, A. Sosinsky, M. A. Crickmore, V. Jacob, A. K. Aggarwal, B. Honig, R. S. Mann
Functional Specificity Of A Hox Protein Mediated By The Recognition Of Minor Groove Structure
Cell(Cambridge, Mass. ) V. 131 530 2007
PubMed-ID: 17981120 | Reference-DOI: 10.1016/J.CELL.2007.09.024
(for further references see the PDB file header)

Molecule 1 - HOMEOTIC PROTEIN SEX COMBS REDUCED
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HOMEOBOX DNA-BINDING DOMAIN
	Gene	:	SCR
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

Molecule 2 - HOMEOBOX PROTEIN EXTRADENTICLE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HOMEOBOX TALE-TYPE DNA-BINDING DOMAIN
	Gene	:	EXD
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	DPBX

*Molecule 3 - DNA (5'- D(DAPDCPDTPDCPDTPDAPDTPDGPDAPDTPDTPDTPDAPDTP DGPDGPDGPDCPDTPDG)-3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

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

		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 2R5Y)

(no "Site" information available for 2R5Y)

(no "SS Bond" information available for 2R5Y)

(no "Cis Peptide Bond" information available for 2R5Y)

(no "SAP(SNP)/Variant" information available for 2R5Y)

Asymmetric/Biological Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	EXD_DROME	274-297	1	B:234-257
1	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	SCR_DROME	357-380	1	A:134-157
2	ANTENNAPEDIA	PS00032	'Homeobox' antennapedia-type protein signature.	SCR_DROME	304-309	1	A:81-86
3	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	SCR_DROME	322-382	1	A:104-159

(no "Exon" information available for 2R5Y)

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
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Chain A from PDB  Type:PROTEIN  Length:73
 aligned with SCR_DROME | P09077 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:88
                                   306       316       326       336       346       356       366       376        
           SCR_DROME    297 GKKNPPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK  384
               SCOP domains d2r5ya_ A: auto               mated matches                                              SCOP domains
               CATH domains 2r5yA00 A:74-16               1 Homeodomain-like                                         CATH domains
               Pfam domains ------------------------------Homeobox-2r5yA01 A:104-158                             --- Pfam domains
         Sec.struct. author ........hhhhh..---------------.....hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------ANTENN------------HOMEOBOX_2  PDB: A:104-159 UniProt: 322-382                  -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------HOMEOBOX_1              ---- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                2r5y A   74 GKKNPPQIYPWMKRV---------------QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK  161
                                    83    |    -         -|      113       123       133       143       153        
                                         88             104

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with EXD_DROME | P40427 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:59
                                   251       261       271       281       291         
           EXD_DROME    242 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNI  300
               SCOP domains d2r5yb_ B: automated matches                                SCOP domains
               CATH domains 2r5yB00 B:205-260 Homeodomain-like                          CATH domains
               Pfam domains Homeobox-2r5yB01 B:205-258                               -- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HOMEOBOX_1              --- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                2r5y B  205 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNI  260
                                   214      1223 ||    231       241       251         
                                            223| ||                                    
                                            1223 ||                                    
                                              1225|                                    
                                                224

Chain C from PDB  Type:DNA  Length:20
                                                     
                2r5y C    1 ACTCTATGATTTATGGGCTG   20
                                    10        20

Chain D from PDB  Type:DNA  Length:20
                                                     
                2r5y D   21 TCAGCCCATAAATCATAGAG   40
                                    30        40

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(

)

Folds(

)

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: automated matches (13)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (5)

1a	d2r5ya_	A:
1b	d2r5yb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	2r5yB00	B:205-260
1b	2r5yA00	A:74-161

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Homeobox (36)

Drosophila melanogaster (Fruit fly) (16)

1a	Homeobox-2r5yB01	B:205-258
1b	Homeobox-2r5yA01	A:104-158

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SCR_DROME | P09077)

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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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: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: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: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:0007379	segment specification	The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes.
	GO:0045498	sex comb development	The process whose specific outcome is the progression of the sex comb over time, from its formation to the mature structure. The sex combs are the male specific chaetae located on the prothoracic tarsal segment of the prothoracic leg.
	GO:0007548	sex differentiation	The establishment of the sex of an organism by physical differentiation.
	GO:0007381	specification of segmental identity, labial segment	The specification of the characteristic structures of the labial segment following establishment of segment boundaries. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
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.

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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	2r5y
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	SCR_DROME \| P09077
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UniProtKB/Swiss-Prot
	EXD_DROME \| P40427	:	1b8i 2r5z 4cyc 4uus
	SCR_DROME \| P09077	:	2r5z

1b8i	STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX
2r5z	STRUCTURE OF SCR/EXD COMPLEX BOUND TO A DNA SEQUENCE DERIVED FROM THE FKH GENE

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