1QSZ - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   THE VEGF-BINDING DOMAIN OF FLT-1 (MINIMIZED MEAN)

Authors :   M. A. Starovasnik, H. W. Christinger, C. Wiesmann, M. A. Champe, A. M. De Vos, N. J. Skelton

Date :   24 Jun 99 (Deposition) - 10 Nov 99 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   Immunoglobulin-Like Domain, I-Set, Vegf Receptor, Hormone/Growth Factor Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Starovasnik, H. W. Christinger, C. Wiesmann, M. A. Champe, A. M. De Vos, N. J. Skelton
Solution Structure Of The Vegf-Binding Domain Of Flt-1: Comparison Of Its Free And Bound States.
J. Mol. Biol. V. 293 531 1999
PubMed-ID: 10543948 | Reference-DOI: 10.1006/JMBI.1999.3134
(for further references see the PDB file header)

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MODIFIED QIAGEN PQE30 CONTAINING HIS-TAG AND GENENASE CLEAVAGE SITE
	Synonym	:	FLT-1


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1QSZ)

NMR Structure

No.	Residues
1	A:158	-	A:207

NMR Structure

No.	Residues
1	Phe A:172	-	Pro A:173

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_042046	E	144	K	VGFR1_HUMAN	Polymorphism	55974987	A	E	144	K

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

(no "PROSITE Motif" information available for 1QSZ)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000282397	1	ENSE00001249591	chr13:29069232-29068917	316	VGFR1_HUMAN	1-22	22	0	-	-
1.2	ENST00000282397	2	ENSE00000938500	chr13:29041754-29041658	97	VGFR1_HUMAN	22-54	33	0	-	-
1.3	ENST00000282397	3	ENSE00000938501	chr13:29041266-29041040	227	VGFR1_HUMAN	54-130	77	1	A:129-130	2
1.4	ENST00000282397	4	ENSE00000906630	chr13:29012482-29012358	125	VGFR1_HUMAN	130-171	42	1	A:130-171	42
1.5	ENST00000282397	5	ENSE00000906629	chr13:29008357-29008195	163	VGFR1_HUMAN	172-226	55	1	A:172-226	55
1.6	ENST00000282397	6	ENSE00000906628	chr13:29008092-29007956	137	VGFR1_HUMAN	226-271	46	1	A:226-229	4
1.7	ENST00000282397	7	ENSE00000906627	chr13:29005447-29005273	175	VGFR1_HUMAN	272-330	59	0	-	-
1.8	ENST00000282397	8	ENSE00000906626	chr13:29004304-29004187	118	VGFR1_HUMAN	330-369	40	0	-	-
1.9	ENST00000282397	9	ENSE00000906625	chr13:29002058-29001889	170	VGFR1_HUMAN	369-426	58	0	-	-
1.10	ENST00000282397	10	ENSE00000906624	chr13:29001455-29001296	160	VGFR1_HUMAN	426-479	54	0	-	-
1.11	ENST00000282397	11	ENSE00000679737	chr13:28980031-28979917	115	VGFR1_HUMAN	479-517	39	0	-	-
1.12	ENST00000282397	12	ENSE00000679735	chr13:28971205-28971097	109	VGFR1_HUMAN	518-554	37	0	-	-
1.13	ENST00000282397	13	ENSE00001005702	chr13:28964241-28963933	309	VGFR1_HUMAN	554-657	104	0	-	-
1.14	ENST00000282397	14	ENSE00001005684	chr13:28959168-28959022	147	VGFR1_HUMAN	657-706	50	0	-	-
1.15	ENST00000282397	15	ENSE00001005678	chr13:28931822-28931691	132	VGFR1_HUMAN	706-750	45	0	-	-
1.16	ENST00000282397	16	ENSE00001005688	chr13:28919688-28919582	107	VGFR1_HUMAN	750-785	36	0	-	-
1.17	ENST00000282397	17	ENSE00000679727	chr13:28913437-28913305	133	VGFR1_HUMAN	786-830	45	0	-	-
1.18	ENST00000282397	18	ENSE00001005682	chr13:28908266-28908162	105	VGFR1_HUMAN	830-865	36	0	-	-
1.19	ENST00000282397	19	ENSE00000679725	chr13:28903865-28903752	114	VGFR1_HUMAN	865-903	39	0	-	-
1.20	ENST00000282397	20	ENSE00001005685	chr13:28901687-28901599	89	VGFR1_HUMAN	903-932	30	0	-	-
1.21	ENST00000282397	21	ENSE00000679723	chr13:28897083-28896927	157	VGFR1_HUMAN	933-985	53	0	-	-
1.22	ENST00000282397	22	ENSE00000679722	chr13:28896496-28896399	98	VGFR1_HUMAN	985-1017	33	0	-	-
1.23	ENST00000282397	23	ENSE00001761843	chr13:28895722-28895600	123	VGFR1_HUMAN	1018-1058	41	0	-	-
1.24	ENST00000282397	24	ENSE00000679720	chr13:28893671-28893560	112	VGFR1_HUMAN	1059-1096	38	0	-	-
1.25	ENST00000282397	25	ENSE00001005671	chr13:28891734-28891635	100	VGFR1_HUMAN	1096-1129	34	0	-	-
1.26	ENST00000282397	26	ENSE00001005693	chr13:28886235-28886130	106	VGFR1_HUMAN	1129-1164	36	0	-	-
1.27	ENST00000282397	27	ENSE00000679717	chr13:28885869-28885727	143	VGFR1_HUMAN	1165-1212	48	0	-	-
1.28	ENST00000282397	28	ENSE00001005655	chr13:28883064-28882980	85	VGFR1_HUMAN	1212-1240	29	0	-	-
1.29	ENST00000282397	29	ENSE00000679715	chr13:28880909-28880815	95	VGFR1_HUMAN	1241-1272	32	0	-	-
1.30	ENST00000282397	30	ENSE00001157319	chr13:28877505-28874489	3017	VGFR1_HUMAN	1272-1338	67	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
	(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:101
 aligned with VGFR1_HUMAN | P17948 from UniProtKB/Swiss-Prot  Length:1338

    Alignment length:101
                                   138       148       158       168       178       188       198       208       218       228 
          VGFR1_HUMAN   129 SDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTI 229
               SCOP domains d1qsza_ A: Second domain of the Flt-1 receptor                                                        SCOP domains
               CATH domains 1qszA00 A:129-229 Immunoglobulins                                                                     CATH domains
               Pfam domains --------Ig_2-1qszA01 A:137-229                                                                        Pfam domains
         Sec.struct. author ...............eeeee.....eee.....hhhhh.eeee...ee.......eeee...eeee...hhhhheeeeeeee....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------K------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.-----------------------------------------Exon 1.5  PDB: A:172-226 UniProt: 172-226              --- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4  PDB: A:130-171 UniProt: 130-171 ------------------------------------------------------1.6  Transcript 1 (2)
                 1qsz A 129 SDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTI 229
                                   138       148       158       168       178       188       198       208       218       228

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: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: I set domains (152)

Protein domain: Second domain of the Flt-1 receptor (5)

Human (Homo sapiens) [TaxId: 9606] (5)

d1qsza_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1qszA00

A:129-229

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: Ig_2 (52)

Homo sapiens (Human) (39)

Ig_2-1qszA01

A:137-229

NMR Structure(hide GO term definitions)

Chain A (VGFR1_HUMAN | P17948)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0036326	VEGF-A-activated receptor activity	Combining with vascular endothelial growth factor A (VEGF-A) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
	GO:0036327	VEGF-B-activated receptor activity	Combining with vascular endothelial growth factor B (VEGF-B) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
	GO:0019838	growth factor binding	Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0036332	placental growth factor-activated receptor activity	Combining with placental growth factor (PlGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
	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: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:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	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.
	GO:0004714	transmembrane receptor protein tyrosine kinase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
	GO:0005021	vascular endothelial growth factor-activated receptor activity	Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
	GO:0000186	activation of MAPKK activity	The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0048514	blood vessel morphogenesis	The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
	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:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0035924	cellular response to vascular endothelial growth factor stimulus	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 vascular endothelial growth factor stimulus.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0048598	embryonic morphogenesis	The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0002548	monocyte chemotaxis	The movement of a monocyte in response to an external stimulus.
	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:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	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:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0043552	positive regulation of phosphatidylinositol 3-kinase activity	Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0010863	positive regulation of phospholipase C activity	Any process that increases the rate of phospholipase C activity.
	GO:0048661	positive regulation of smooth muscle cell proliferation	Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
	GO:0030949	positive regulation of vascular endothelial growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0006940	regulation of smooth muscle contraction	Any process that modulates the frequency, rate or extent of smooth muscle contraction.
	GO:0001666	response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	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.
	GO:0036323	vascular endothelial growth factor receptor-1 signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-1 (VEGFR-1) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0038084	vascular endothelial growth factor signaling pathway	A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

NMR Structure
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(no "Sites" information available for 1qsz)

	Cis Peptide Bonds
		Phe A:172 - Pro A:173	[ RasMol ]

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	1qsz
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	VGFR1_HUMAN \| P17948
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	VGFR1_HUMAN \| P17948	:	1flt 1qsv 1qty 1rv6 2xac 3hng 4ckv 4cl7 5abd 5ex3 5t89

1flt	1.7 A RESOLUTION CRYSTAL STRUCTURE OF THE SECOND IMMUNOGLOBULIN-LIKE DOMAIN OF FLT-1 IN COMPLEX WITH VEGF
1qsv	ENSEMBLE OF 20 STRUCTURES FROM WHICH THIS MINIMIZED MEAN STRUCTURE WAS DERIVED.

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (1, 1)

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Exons (4, 4)

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