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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE C-TERMINAL SH3 DOMAIN OF P67PHOX COMPLEXED WITH THE C-TERMINAL TAIL REGION OF P47PHOX

Authors :   K. Kami, R. Takeya, H. Sumimoto, D. Kohda

Date :   08 Oct 01 (Deposition) - 08 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : P,S  (22x)

Keywords :   P67Phox, P47Phox, Sh3-Peptide Complex, Helix-Turn-Helix, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kami, R. Takeya, H. Sumimoto, D. Kohda
Diverse Recognition Of Non-Pxxp Peptide Ligands By The Sh3 Domains From P67(Phox), Grb2 And Pex13P.
Embo J. V. 21 4268 2002
PubMed-ID: 12169629 | Reference-DOI: 10.1093/EMBOJ/CDF428
(for further references see the PDB file header)

Molecule 1 - PHAGOCYTE NADPH OXIDASE SUBUNIT P67PHOX
	Chains	:	S
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL SH3 DOMAIN (RESIDUES 455-516)
	Gene	:	NCF2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NEUTROPHIL CYTOSOL FACTOR 2

Molecule 2 - PHAGOCYTE NADPH OXIDASE SUBUNIT P47PHOX
	Chains	:	P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	TAIL PEPTIDE (RESIDUES 359-390)
	Gene	:	NCF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NEUTROPHIL CYTOSOL FACTOR 1


NMR Structure (22x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1K4U)

(no "Site" information available for 1K4U)

(no "SS Bond" information available for 1K4U)

(no "Cis Peptide Bond" information available for 1K4U)

(no "SAP(SNP)/Variant" information available for 1K4U)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	NCF2_HUMAN	240-299 457-516	1	- S:457-516

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000367536	1	ENSE00001444961	chr1:183560011-183559975	37	NCF2_HUMAN	-	0	0	-	-
1.2c	ENST00000367536	2c	ENSE00001444960	chr1:183559494-183559291	204	NCF2_HUMAN	1-58	58	0	-	-
1.3	ENST00000367536	3	ENSE00000774250	chr1:183556112-183556030	83	NCF2_HUMAN	59-86	28	0	-	-
1.4	ENST00000367536	4	ENSE00000922163	chr1:183546842-183546734	109	NCF2_HUMAN	86-122	37	0	-	-
1.5	ENST00000367536	5	ENSE00000922162	chr1:183543756-183543622	135	NCF2_HUMAN	123-167	45	0	-	-
1.6	ENST00000367536	6	ENSE00000922161	chr1:183542427-183542320	108	NCF2_HUMAN	168-203	36	0	-	-
1.7a	ENST00000367536	7a	ENSE00000922160	chr1:183539974-183539915	60	NCF2_HUMAN	204-223	20	0	-	-
1.8b	ENST00000367536	8b	ENSE00000774245	chr1:183538320-183538277	44	NCF2_HUMAN	224-238	15	0	-	-
1.9b	ENST00000367536	9b	ENSE00001592444	chr1:183536480-183536339	142	NCF2_HUMAN	238-285	48	0	-	-
1.10	ENST00000367536	10	ENSE00000774243	chr1:183536123-183536055	69	NCF2_HUMAN	286-308	23	0	-	-
1.11	ENST00000367536	11	ENSE00001738087	chr1:183534914-183534839	76	NCF2_HUMAN	309-334	26	0	-	-
1.12b	ENST00000367536	12b	ENSE00001735809	chr1:183533165-183533140	26	NCF2_HUMAN	334-342	9	0	-	-
1.12c	ENST00000367536	12c	ENSE00001784834	chr1:183532720-183532569	152	NCF2_HUMAN	343-393	51	0	-	-
1.13c	ENST00000367536	13c	ENSE00000922153	chr1:183532441-183532330	112	NCF2_HUMAN	393-430	38	0	-	-
1.14b	ENST00000367536	14b	ENSE00000774239	chr1:183529408-183529231	178	NCF2_HUMAN	431-490	60	1	S:455-490	36
1.15b	ENST00000367536	15b	ENSE00001444959	chr1:183525365-183524698	668	NCF2_HUMAN	490-526	37	1	S:490-516	27

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 P from PDB  Type:PROTEIN  Length:32
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:32
                                   368       378       388  
           NCF1_HUMAN   359 SKPQPAVPPRPSADLILNRCSESTKRKLASAV 390
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains p47_phox_C-1k4uP01 P:359-390     Pfam domains
         Sec.struct. author ...........hhhhhhhh.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 1k4u P 359 SKPQPAVPPRPSADLILNRCSESTKRKLASAV 390
                                   368       378       388

Chain S from PDB  Type:PROTEIN  Length:62
 aligned with NCF2_HUMAN | P19878 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:62
                                   464       474       484       494       504       514  
           NCF2_HUMAN   455 QLKKGSQVEALFSYEATQPEDLEFQEGDIILVLSKVNEEWLEGECKGKVGIFPKVFVEDCAT 516
               SCOP domains d1k4us_ S: p67phox                                             SCOP domains
               CATH domains 1k4uS00 S:455-516 SH3 Domains                                  CATH domains
               Pfam domains --------SH3_1-1k4uS01 S:463-508                       -------- Pfam domains
         Sec.struct. author .....eeee...................eeeeeee.....eeee....eeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SH3  PDB: S:457-516 UniProt: 457-516                         PROSITE
           Transcript 1 (1) Exon 1.14b  PDB: S:455-490          -------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.15b  PDB: S:490-516  Transcript 1 (2)
                 1k4u S 455 QLKKGSQVEALFSYEATQPEDLEFQEGDIILVLSKVNEEWLEGESKGKVGIFPKVFVEDSAT 516
                                   464       474       484       494       504       514

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 beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: SH3-domain (369)

Family: SH3-domain (255)

Protein domain: p67phox (2)

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

d1k4us_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Human (Homo sapiens) (133)

1k4uS00

S:455-516

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SH3 (175)

Family: SH3_1 (141)

Homo sapiens (Human) (69)

SH3_1-1k4uS01

S:463-508

Clan: no clan defined [family: p47_phox_C] (2)

Family: p47_phox_C (2)

Homo sapiens (Human) (2)

p47_phox_C-1k4uP01

P:359-390

NMR Structure(hide GO term definitions)

Chain P (NCF1_HUMAN | P14598)

molecular function
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0043325	phosphatidylinositol-3,4-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
	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:0016175	superoxide-generating NADPH oxidase activity	Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-.
biological process
	GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006968	cellular defense response	A defense response that is mediated by cells.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
	GO:0045730	respiratory burst	A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
	GO:0042554	superoxide anion generation	The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways.
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0043020	NADPH oxidase complex	A enzyme complex of which the core is a heterodimer composed of a light (alpha) and heavy (beta) chain, and requires several other water-soluble proteins of cytosolic origin for activity. Functions in superoxide generation by the NADPH-dependent reduction of O2.
	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:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0032010	phagolysosome	A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.

Chain S (NCF2_HUMAN | P19878)

molecular function
	GO:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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: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:0016175	superoxide-generating NADPH oxidase activity	Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-.
biological process
	GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006968	cellular defense response	A defense response that is mediated by cells.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0045730	respiratory burst	A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
	GO:0042554	superoxide anion generation	The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways.
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0043020	NADPH oxidase complex	A enzyme complex of which the core is a heterodimer composed of a light (alpha) and heavy (beta) chain, and requires several other water-soluble proteins of cytosolic origin for activity. Functions in superoxide generation by the NADPH-dependent reduction of O2.
	GO:0001669	acrosomal vesicle	A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
	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:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0032010	phagolysosome	A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.

NMR Structure
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	NCF1_HUMAN \| P14598	:	1gd5 1kq6 1ng2 1o7k 1ov3 1uec 1w70 1wlp
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