3L2C - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF FOXO4 BOUND TO DNA

Authors :   E. Boura, J. Silhan, M. Sulc, J. Brynda, V. Obsilova, T. Obsil

Date :   15 Dec 09 (Deposition) - 29 Dec 09 (Release) - 22 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

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

Keywords :   Forkhead, Forkhead Box, Winged Helix, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Boura, L. Rezabkova, J. Brynda, V. Obsilova, T. Obsil
Structure Of The Human Foxo4-Dbd-Dna Complex At 1. 9 A Resolution Reveals New Details Of Foxo Binding To The Dna
Acta Crystallogr. , Sect. D V. 66 1351 2010
PubMed-ID: 21123876 | Reference-DOI: 10.1107/S0907444910042228

Molecule 1 - FOXO CONSENSUS BINDING SEQUENCE, PLUS STRAND
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SYNTHETIC DNA
	Synthetic	:	YES

Molecule 2 - FOXO CONSENSUS BINDING SEQUENCE, MINUS STRAND
	Chains	:	C
	Engineered	:	YES
	Other Details	:	SYNTHETIC DNA
	Synthetic	:	YES

Molecule 3 - FORKHEAD BOX PROTEIN O4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN, UNP RESIDUES 86-187
	Gene	:	AFX, AFX1, FOXO4, MLLT7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FORKHEAD TRANSCRIPTION FACTOR FOXO4, FORK HEAD DOMAIN TRANSCRIPTION FACTOR AFX1

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:154 , SER A:155 , HIS A:157 , PHE A:160 , HOH C:60	BINDING SITE FOR RESIDUE MG A 1
2	AC2	SOFTWARE	DT C:35 , HOH C:70 , HOH C:71 , HOH C:72 , HOH C:73 , HOH C:74	BINDING SITE FOR RESIDUE MG C 2

(no "SS Bond" information available for 3L2C)

(no "Cis Peptide Bond" information available for 3L2C)

(no "SAP(SNP)/Variant" information available for 3L2C)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FORK_HEAD_3	PS50039	Fork head domain profile.	FOXO4_HUMAN	101-195	1	A:97-177
2	FORK_HEAD_2	PS00658	Fork head domain signature 2.	FOXO4_HUMAN	150-156	1	A:146-152

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000374259	1a	ENSE00001892186	X:70316047-70316831	785	FOXO4_HUMAN	1-151	151	1	A:93-147	55
1.3c	ENST00000374259	3c	ENSE00001321000	X:70320534-70321590	1057	FOXO4_HUMAN	152-504	353	1	A:148-177	30
1.4c	ENST00000374259	4c	ENSE00001462943	X:70321927-70323385	1459	FOXO4_HUMAN	504-505	2	0	-	-

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:85
 aligned with FOXO4_HUMAN | P98177 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:85
                                   106       116       126       136       146       156       166       176     
          FOXO4_HUMAN    97 RRNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNEATGKSSWWMLN 181
               SCOP domains d3l2ca_ A: Afx (Foxo4)                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fork_head-3l2cA01 A:93-177                                                            Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..eeee.........eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----FORK_HEAD_3  PDB: A:97-177 UniProt: 101-195                                       PROSITE (1)
                PROSITE (2) -----------------------------------------------------FORK_HE------------------------- PROSITE (2)
               Transcript 1 Exon 1.1a  PDB: A:93-147 UniProt: 1-151 [INCOMPLETE]   Exon 1.3c  PDB: A:148-177      Transcript 1
                 3l2c A  93 RRNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNEATGKSSWWMLN 177
                                   102       112       122       132       142       152       162       172

Chain B from PDB  Type:DNA  Length:13
                                             
                 3l2c B   1 CTATGTAAACAAC  13
                                    10

Chain C from PDB  Type:DNA  Length:13
                                             
                 3l2c C  25 GTTGTTTACATAG  37
                                    34

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: Winged helix DNA-binding domain (576)

Family: Forkhead DNA-binding domain (17)

Protein domain: Afx (Foxo4) (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d3l2ca_

(no "CATH Domain" information available for 3L2C)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Fork_head] (7)

Family: Fork_head (7)

Homo sapiens (Human) (6)

Fork_head-3l2cA01

A:93-177

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FOXO4_HUMAN | P98177)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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.
	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:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0008286	insulin receptor signaling pathway	The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
	GO:0007095	mitotic G2 DNA damage checkpoint	A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage.
	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:0007517	muscle organ development	The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
	GO:0070317	negative regulation of G0 to G1 transition	A cell cycle process that stops, prevents, or reduces the rate or extent of the transition from the G0 quiescent state to the G1 phase.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0051151	negative regulation of smooth muscle cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation.
	GO:0071158	positive regulation of cell cycle arrest	Any process that increases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048863	stem cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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