2K40 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR STRUCTURE OF HESX-1 HOMEODOMAIN DOUBLE MUTANT R31L/E42L

Authors :   J. Asensio, M. Torrado, C. Gonzalez, A. Bastida

Date :   26 May 08 (Deposition) - 05 May 09 (Release) - 05 May 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Thermostable Homeodomain Variant, Dna Binding Protein, Developmental Protein, Disease Mutation, Dna-Binding, Dwarfism, Homeobox, Nucleus, Polymorphism, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Asensio, M. Torrado, C. Gonzalez, A. Bastida, F. Corzana
The Role Of Conserved Salt-Bridges On Homeodomain Stability
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HOMEOBOX EXPRESSED IN ES CELLS 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PT7-7
	Fragment	:	DNA BINDING DOMAIN OF HUMAN TRANSCRIPTION FACTOR HESX-I (UNP RESIDUES 108-174)
	Gene	:	HESX1, HANF
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HOMEOBOX PROTEIN ANF, HANF


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2K40)

(no "Site" information available for 2K40)

(no "SS Bond" information available for 2K40)

(no "Cis Peptide Bond" information available for 2K40)

NMR Structure (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_078488	R	109	Q	HESX1_HUMAN	Unclassified (CPHD5)	---	A	R	2	Q
2	UniProt	VAR_010400	N	125	S	HESX1_HUMAN	Polymorphism	9878928	A	N	18	S
3	UniProt	VAR_063232	E	149	K	HESX1_HUMAN	Disease (GHDPA)	104893742	A	L	42	K
4	UniProt	VAR_010225	R	160	C	HESX1_HUMAN	Disease (SOD)	28936702	A	R	53	C
5	UniProt	VAR_063233	S	170	L	HESX1_HUMAN	Disease (SOD)	28936703	A	S	63	L

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	HESX1_HUMAN	141-164	1	A:34-57

(no "Exon" information available for 2K40)

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:67
 aligned with HESX1_HUMAN | Q9UBX0 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:67
                                   117       127       137       147       157       167       
          HESX1_HUMAN   108 GRRPRTAFTQNQIEVLENVFRVNCYPGIDIREDLAQKLNLEEDRIQIWFQNRRAKLKRSHRESQFLM 174
               SCOP domains d2k40a_ A: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains -Homeobox-2k40A01 A:2-58                                  --------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -Q---------------S-----------------------K----------C---------L---- SAPs(SNPs)
                    PROSITE ---------------------------------HOMEOBOX_1  PDB: A:34-57---------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2k40 A   1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQFLM  67
                                    10        20        30        40        50        60

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

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

Superfamily: Homeodomain-like (373)

Family: automated matches (53)

Protein domain: automated matches (53)

Human (Homo sapiens) [TaxId: 9606] (19)

d2k40a_

(no "CATH Domain" information available for 2K40)

NMR Structure

Clans(

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Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Homeobox (36)

Homo sapiens (Human) (9)

Homeobox-2k40A01

A:2-58

NMR Structure(hide GO term definitions)

Chain A (HESX1_HUMAN | Q9UBX0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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.
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:0048853	forebrain morphogenesis	The process in which the anatomical structures of the forebrain are generated and organized. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
	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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043584	nose development	The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity).
	GO:0030916	otic vesicle formation	The process resulting in the transition of the otic placode into the otic vesicle, a transient embryonic structure formed during development of the vertebrate inner ear.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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.

NMR Structure
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