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Description

Title :   COMPLEX OF THE KH3 AND KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29MER DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE

Authors :   G. M. Clore, D. T. Braddock

Date :   30 Nov 01 (Deposition) - 06 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B

Keywords :   Single-Stranded Dna Binding Protein, Transcription Factor, Fbp, Fuse Element, C-Myc Oncogene, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. T. Braddock, J. M. Louis, J. L. Baber, D. Levens, G. M. Clore
Structure And Dynamics Of Kh Domains From Fbp Bound To Single-Stranded Dna.
Nature V. 415 1051 2002
PubMed-ID: 11875576 | Reference-DOI: 10.1038/4151051A
(for further references see the PDB file header)

Compounds

Molecule 1 - FUSE BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BE23
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 278-447, NUMBERERED 5-174. KH3 AND KH4 DOMAINS.
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FBP, FAR UPSTREAM BINDING ELEMENT PROTEIN

*Molecule 2 - DNA (5'- D(GPTPATPAPTPTPCPCPCPTPCPGPGPGAPTPTPTPT PTPTPAPTPTPTPTPGPT)-3')**
	Chains	:	B
	Engineered	:	YES
	Other Details	:	FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE
	Synthetic	:	YES

Structural Features

Chains, Units


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J4W)

Sites (0, 0)

(no "Site" information available for 1J4W)

SS Bonds (0, 0)

(no "SS Bond" information available for 1J4W)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1J4W)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049679	I	399	K	FUBP1_HUMAN	Polymorphism	12748509	A	I	126	K

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

PROSITE Motifs (1, 2)

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	FUBP1_HUMAN	100-164 185-251 275-339 376-443	2	- - A:5-66 A:104-170

Exons (5, 5)

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1e	ENST00000370768	1e	ENSE00001815368	chr1:78444770-78444569	202	FUBP1_HUMAN	1-40	40	0	-	-
1.2	ENST00000370768	2	ENSE00001066871	chr1:78435699-78435609	91	FUBP1_HUMAN	41-71	31	0	-	-
1.4	ENST00000370768	4	ENSE00001066882	chr1:78433887-78433849	39	FUBP1_HUMAN	71-84	14	0	-	-
1.5	ENST00000370768	5	ENSE00001066879	chr1:78433350-78433311	40	FUBP1_HUMAN	84-97	14	0	-	-
1.6a	ENST00000370768	6a	ENSE00001349606	chr1:78432785-78432733	53	FUBP1_HUMAN	97-115	19	0	-	-
1.7	ENST00000370768	7	ENSE00001066887	chr1:78432639-78432568	72	FUBP1_HUMAN	115-139	25	0	-	-
1.8	ENST00000370768	8	ENSE00001066874	chr1:78432435-78432378	58	FUBP1_HUMAN	139-158	20	0	-	-
1.9	ENST00000370768	9	ENSE00002163081	chr1:78430915-78430753	163	FUBP1_HUMAN	158-212	55	0	-	-
1.10	ENST00000370768	10	ENSE00001066888	chr1:78430653-78430555	99	FUBP1_HUMAN	213-245	33	0	-	-
1.11	ENST00000370768	11	ENSE00001066872	chr1:78430432-78430331	102	FUBP1_HUMAN	246-279	34	1	A:1-6	6
1.12	ENST00000370768	12	ENSE00001066883	chr1:78430041-78429939	103	FUBP1_HUMAN	280-314	35	1	A:7-41	35
1.13	ENST00000370768	13	ENSE00001066884	chr1:78429847-78429747	101	FUBP1_HUMAN	314-347	34	1	A:41-74	34
1.14	ENST00000370768	14	ENSE00001435529	chr1:78429400-78429259	142	FUBP1_HUMAN	348-395	48	1	A:104-122	19
1.15	ENST00000370768	15	ENSE00001435707	chr1:78428615-78428455	161	FUBP1_HUMAN	395-448	54	1	A:122-174	53
1.16b	ENST00000370768	16b	ENSE00001066870	chr1:78426180-78426029	152	FUBP1_HUMAN	449-499	51	0	-	-
1.17	ENST00000370768	17	ENSE00001066877	chr1:78425948-78425869	80	FUBP1_HUMAN	499-526	28	0	-	-
1.18	ENST00000370768	18	ENSE00001066876	chr1:78422385-78422257	129	FUBP1_HUMAN	526-569	44	0	-	-
1.19d	ENST00000370768	19d	ENSE00001066889	chr1:78421014-78420940	75	FUBP1_HUMAN	569-594	26	0	-	-
1.20a	ENST00000370768	20a	ENSE00001349579	chr1:78414985-78414840	146	FUBP1_HUMAN	594-642	49	0	-	-
1.21b	ENST00000370768	21b	ENSE00001916670	chr1:78414459-78414090	370	FUBP1_HUMAN	643-644	2	0	-	-

Sequences/Alignments

NMR Structure

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:145
 aligned with FUBP1_HUMAN | Q96AE4 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:174
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443    
          FUBP1_HUMAN   274 GNEGIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRCQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 447
               SCOP domains d1j4wa1 A:1-74 Far upstream binding element, FBP                          -----------------------------d1j4wa2 A:104-174 Far upstream binding element, FBP                     SCOP domains
               CATH domains 1j4wA01 A:1-74  [code=3.30.1370.10, no name defined]                      -----------------------------1j4wA02 A:104-174  [code=3.30.1370.10, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeeee.......eeeeeeeehhhhhhhhhhhhhhhhhhhh-----------------------------.eeeeeee..hhhhhhh..hhhhhhhhhhhh.eeeee..........eeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------K------------------------------------------------ SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: A:5-66 UniProt: 275-339                          ------------------------------------KH_TYPE_1  PDB: A:104-170 UniProt: 376-443                          ---- PROSITE
           Transcript 1 (1) 1.11  Exon 1.12  PDB: A:7-41             ---------------------------------Exon 1.14  PDB: A:104-122 UniProt: 348-395      ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.13  PDB: A:41-74           -----------------------------------------------Exon 1.15  PDB: A:122-174 UniProt: 395-448            Transcript 1 (2)
                 1j4w A   1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQ-----------------------------QEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174
                                    10        20        30        40        50        60        70   |     -         -         -   |   110       120       130       140       150       160       170    
                                                                                                    74                           104

Chain B from PDB  Type:DNA  Length:15
                                               
                 1j4w B 204 TATTCCCTATTTTTT 222
                                   217     
                                 211|      
                                  216

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Eukaryotic type KH-domain (KH-domain type I) (51)

Superfamily: Eukaryotic type KH-domain (KH-domain type I) (51)

Family: Eukaryotic type KH-domain (KH-domain type I) (40)

Protein domain: Far upstream binding element, FBP (3)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1j4wa1	A:1-74
1b	d1j4wa2	A:104-174

CATH Domains (1, 2)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal Protein S8; Chain: A, domain 1 (139)

Homologous Superfamily: [code=3.30.1370.10, no name defined] (23)

Human (Homo sapiens) (13)

1a	1j4wA02	A:104-174
1b	1j4wA01	A:1-74

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1J4W)

Gene Ontology (12, 12)

NMR Structure(hide GO term definitions)

Chain A (FUBP1_HUMAN | Q96AE4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	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:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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: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.

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Related Entries

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UniProtKB/Swiss-Prot
	FUBP1_HUMAN \| Q96AE4	:	2kxh 4lij

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