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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE HOMEOBOX DOMAIN OF HUMAN HOMEOBOX PROTEIN PKNOX1

Authors :   Y. O. Kamatari, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   26 Apr 05 (Deposition) - 26 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Homeobox Domain, Human Homeobox Protein Pknox1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. O. Kamatari, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Pknox1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HOMEOBOX PROTEIN PKNOX1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040628-06
	Expression System Vector Type	:	PLASMID
	Fragment	:	HOMEOBOX DOMAIN
	Gene	:	PKNOX1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	PBX/KNOTTED HOMEOBOX 1, HOMEOBOX PROTEIN PREP-1


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1X2N)

(no "Site" information available for 1X2N)

(no "SS Bond" information available for 1X2N)

(no "Cis Peptide Bond" information available for 1X2N)

NMR Structure (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036440	V	265	I	PKNX1_HUMAN	Unclassified	376883451	A	V	13	I
2	CancerSNP	VAR_PKNX1_HUMAN_CCDS13692_1_01 *	V	265	I	PKNX1_HUMAN	Disease (Colorectal cancer)	---	A	V	13	I
	* ID not provided by source

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	PKNX1_HUMAN	257-320	1	A:6-67

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000291547	1a	ENSE00001860427	chr21:44394620-44394774	155	PKNX1_HUMAN	-	0	0	-	-
1.2	ENST00000291547	2	ENSE00002153862	chr21:44424436-44424542	107	PKNX1_HUMAN	1-17	17	0	-	-
1.3	ENST00000291547	3	ENSE00001050485	chr21:44427601-44427728	128	PKNX1_HUMAN	18-60	43	0	-	-
1.4	ENST00000291547	4	ENSE00001050478	chr21:44430163-44430334	172	PKNX1_HUMAN	60-117	58	0	-	-
1.5	ENST00000291547	5	ENSE00001050481	chr21:44433178-44433348	171	PKNX1_HUMAN	118-174	57	1	A:1-5	5
1.6a	ENST00000291547	6a	ENSE00001050484	chr21:44437018-44437117	100	PKNX1_HUMAN	175-208	34	0	-	-
1.7	ENST00000291547	7	ENSE00001050476	chr21:44438243-44438340	98	PKNX1_HUMAN	208-240	33	0	-	-
1.8b	ENST00000291547	8b	ENSE00001050480	chr21:44441413-44441541	129	PKNX1_HUMAN	241-283	43	1	A:6-31	26
1.9	ENST00000291547	9	ENSE00001050482	chr21:44444981-44445057	77	PKNX1_HUMAN	284-309	26	1	A:32-57	26
1.10b	ENST00000291547	10b	ENSE00001050479	chr21:44448812-44448984	173	PKNX1_HUMAN	309-367	59	1	A:57-73 (gaps)	59
1.11a	ENST00000291547	11a	ENSE00001050477	chr21:44450000-44453692	3693	PKNX1_HUMAN	367-436	70	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:73
 aligned with PKNX1_HUMAN | P55347 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:206
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      
          PKNX1_HUMAN   162 GEPGSPYSPVQSQQIQSAITGTISPQGIVVPASALQQGNVAMATVAGGTVYQPVTVVTPQGQVVTQTLSPGTIRIQNSQLQLQLNQDLSILHQDDGSSKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQPMLDSSCSETPKTKKKTAQNRPVQRFWPDSIASGVAQPPPSELTMSEG 367
               SCOP domains ------------------------------------------------------------------------------------------------d1x2na1 A:6-67 Homeobox protein pknox1                        ------------------------------------------------ SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------Homeobox_KN-1x2nA01 A:25-64             --------------------------------------------------- Pfam domains
         Sec.struct. author .....-------------------------------------------------------------------------------------------.........hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh--------------------------------h.----...------. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------HOMEOBOX_2  PDB: A:6-67 UniProt: 257-320                        ----------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5     Exon 1.6a  PDB: - UniProt: 175-208--------------------------------Exon 1.8b  PDB: A:6-31 UniProt: 241-283    -------------------------Exon 1.10b  PDB: A:57-73 (gaps) UniProt: 309-367            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.7  PDB: - UniProt: 208-240-------------------------------------------Exon 1.9  PDB: A:32-57    ---------------------------------------------------------1 Transcript 1 (2)
                 1x2n A   1 GSSGS-------------------------------------------------------------------------------------------SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ--------------------------------SG----PSS------G  73
                                |    -         -         -         -         -         -         -         -         -      |  9        19        29        39        49        59       | -         -         -         -||    | |-     |
                                5                                                                                           6                                                           67                               68|   70 |     73
                                                                                                                                                                                                                          69     72

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 '\|'

NMR Structure

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: Homeobox protein pknox1 (1)

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

d1x2na1

A:6-67

(no "CATH Domain" information available for 1X2N)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Homeobox_KN (2)

Homo sapiens (Human) (2)

Homeobox_KN-1x2nA01

A:25-64

NMR Structure(hide GO term definitions)

Chain A (PKNX1_HUMAN | P55347)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0043010	camera-type eye development	The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
	GO:0030218	erythrocyte differentiation	The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	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: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: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).
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.

NMR Structure
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