2L05 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION NMR STRUCTURE OF THE RAS-BINDING DOMAIN OF SERINE/THREONINE-PROTEIN KINASE B-RAF FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR4694F

Authors :   J. M. Aramini, H. Janjua, C. Ciccosanti, R. Shastry, Y. J. Huang, T. B. Ac R. Xiao, J. K. Everett, G. T. Montelione, Northeast Structural Geno Consortium (Nesg)

Date :   30 Jun 10 (Deposition) - 14 Jul 10 (Release) - 14 Jul 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Structural Genomics, Northeast Structural Genomics Consortium (Nesg), Psi-2, Protein Structure Initiative, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Aramini, H. Janjua, C. Ciccosanti, R. Shastry, Y. J. Huang, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione
Solution Nmr Structure Of The Ras-Binding Domain Of Serine/Threonine-Protein Kinase B-Raf From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr4694F
To Be Published
PubMed: search

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PMGK
	Expression System Taxid	:	469008
	Expression System Vector	:	PET 14-15C
	Fragment	:	RBD DOMAIN RESIDUES 149-232
	Gene	:	BRAF, BRAF1, RAFB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTO-ONCOGENE B-RAF, P94, V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2L05)

(no "Site" information available for 2L05)

(no "SS Bond" information available for 2L05)

(no "Cis Peptide Bond" information available for 2L05)

(no "SAP(SNP)/Variant" information available for 2L05)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RBD	PS50898	Ras-binding domain (RBD) profile.	BRAF_HUMAN	155-227	1	A:155-227

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RBD	PS50898	Ras-binding domain (RBD) profile.	BRAF_HUMAN	155-227	1	A:155-227

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000288602	1a	ENSE00001154485	chr7:140624564-140624366	199	BRAF_HUMAN	1-46	46	0	-	-
1.2	ENST00000288602	2	ENSE00001035281	chr7:140550012-140549911	102	BRAF_HUMAN	47-80	34	0	-	-
1.3a	ENST00000288602	3a	ENSE00001035295	chr7:140534672-140534409	264	BRAF_HUMAN	81-168	88	1	A:147-168	22
1.4	ENST00000288602	4	ENSE00001034889	chr7:140508795-140508692	104	BRAF_HUMAN	169-203	35	1	A:169-203	35
1.6	ENST00000288602	6	ENSE00001034814	chr7:140507862-140507760	103	BRAF_HUMAN	203-237	35	1	A:203-232	30
1.7	ENST00000288602	7	ENSE00001034880	chr7:140501360-140501212	149	BRAF_HUMAN	238-287	50	0	-	-
1.8	ENST00000288602	8	ENSE00001034818	chr7:140500281-140500162	120	BRAF_HUMAN	287-327	41	0	-	-
1.9	ENST00000288602	9	ENSE00001034830	chr7:140494267-140494108	160	BRAF_HUMAN	327-380	54	0	-	-
1.10	ENST00000288602	10	ENSE00001034865	chr7:140487384-140487348	37	BRAF_HUMAN	381-393	13	0	-	-
1.11	ENST00000288602	11	ENSE00001034844	chr7:140482957-140482821	137	BRAF_HUMAN	393-438	46	0	-	-
1.12	ENST00000288602	12	ENSE00001034859	chr7:140481493-140481376	118	BRAF_HUMAN	439-478	40	0	-	-
1.13	ENST00000288602	13	ENSE00001034883	chr7:140477875-140477791	85	BRAF_HUMAN	478-506	29	0	-	-
1.14	ENST00000288602	14	ENSE00001034826	chr7:140476888-140476712	177	BRAF_HUMAN	506-565	60	0	-	-
1.15a	ENST00000288602	15a	ENSE00001034811	chr7:140454033-140453987	47	BRAF_HUMAN	565-581	17	0	-	-
1.16	ENST00000288602	16	ENSE00001034798	chr7:140453193-140453075	119	BRAF_HUMAN	581-620	40	0	-	-
1.17	ENST00000288602	17	ENSE00001034817	chr7:140449218-140449087	132	BRAF_HUMAN	621-664	44	0	-	-
1.19	ENST00000288602	19	ENSE00001034824	chr7:140439746-140439612	135	BRAF_HUMAN	665-709	45	0	-	-
1.20d	ENST00000288602	20d	ENSE00001034876	chr7:140434570-140434279	292	BRAF_HUMAN	710-766	57	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)
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Chain A from PDB  Type:PROTEIN  Length:86
 aligned with BRAF_HUMAN | P15056 from UniProtKB/Swiss-Prot  Length:766

    Alignment length:86
                                   156       166       176       186       196       206       216       226      
           BRAF_HUMAN   147 SNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDSLKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPL 232
               SCOP domains d2l05a_ A: automated matches                                                           SCOP domains
               CATH domains ---------2l05A01 A:156-226                                                      ------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee...eeeeee.....hhhhhhhhhhhhhh.hhh.eeeeeee..eeeee....hhhhhh..eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------RBD  PDB: A:155-227 UniProt: 155-227                                     ----- PROSITE
           Transcript 1 (1) Exon 1.3a [INCOMPLETE]Exon 1.4  PDB: A:169-203           ----------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.6  PDB: A:203-232       Transcript 1 (2)
                 2l05 A 147 HMPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDSLKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPL 232
                                   156       166       176       186       196       206       216       226

Legend:		→ Mismatch	(orange background)
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	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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: automated matches (55)

Protein domain: automated matches (55)

Human (Homo sapiens) [TaxId: 9606] (39)

d2l05a_

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 (286)

Human (Homo sapiens) (177)

2l05A01

A:156-226

(no "Pfam Domain" information available for 2L05)

NMR Structure(hide GO term definitions)

Chain A (BRAF_HUMAN | P15056)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004709	MAP kinase kinase kinase activity	Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0031434	mitogen-activated protein kinase kinase binding	Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase, any protein that can phosphorylate a MAP kinase.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0005057	signal transducer activity, downstream of receptor	Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
	GO:0031267	small GTPase binding	Interacting selectively and non-covalently with a small monomeric GTPase.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0043367	CD4-positive, alpha-beta T cell differentiation	The process in which a relatively unspecialized T cell acquires specialized features of a mature CD4-positive, alpha-beta T cell.
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0000186	activation of MAPKK activity	The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
	GO:0046632	alpha-beta T cell differentiation	The process in which a precursor cell type acquires the specialized features of an alpha-beta T cell. An alpha-beta T cell is a T cell that expresses an alpha-beta T cell receptor complex.
	GO:0009887	animal organ morphogenesis	Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
	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:0071277	cellular response to calcium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0090150	establishment of protein localization to membrane	The directed movement of a protein to a specific location in a membrane.
	GO:0060324	face development	The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
	GO:0015758	glucose transport	The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0060323	head morphogenesis	The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0060291	long-term synaptic potentiation	A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.
	GO:0002318	myeloid progenitor cell differentiation	The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:2000352	negative regulation of endothelial cell apoptotic process	Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
	GO:0010764	negative regulation of fibroblast migration	Any process that decreases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:2000301	negative regulation of synaptic vesicle exocytosis	Any process that stops, prevents or reduces the frequency, rate or extent of synaptic vesicle exocytosis.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0043368	positive T cell selection	The process of sparing immature T cells which react with self-MHC protein complexes with low affinity levels from apoptotic death.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0048680	positive regulation of axon regeneration	Any process that activates, maintains or increases the rate of axon regeneration.
	GO:0050772	positive regulation of axonogenesis	Any process that activates or increases the frequency, rate or extent of axonogenesis.
	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:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0051496	positive regulation of stress fiber assembly	Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	GO:1900026	positive regulation of substrate adhesion-dependent cell spreading	Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
	GO:0051291	protein heterooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0048679	regulation of axon regeneration	Any process that modulates the frequency, rate or extent of axon regeneration.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0051591	response to cAMP	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0043434	response to peptide hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0035019	somatic stem cell population maintenance	Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
	GO:0048538	thymus development	The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
	GO:0030878	thyroid gland development	The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone.
	GO:0008542	visual learning	Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
	GO:0044297	cell body	The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
	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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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	2l05
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