3Q90 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE NTF2 DOMAIN OF RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1

Authors :   M. Welin, L. Tresaugues, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, T. Ekblad, S. Flodin, A. Flores, S. Graslund, M. Hammars I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Mo T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorse Der Berg, E. Wahlberg, J. Weigelt, P. Nordlund, Structural Genomic Consortium (Sgc)

Date :   07 Jan 11 (Deposition) - 16 Feb 11 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Ntf2-Like (A+B Proteins), Protein Binding And Helicase, Protein (Ras Gtpase- Activating Protein), Dna And Rna Binding, Plasma Membrane, Nucleus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, L. Tresaugues, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, T. Ekblad, S. Flodin, A. Flores, S. Graslund M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, P. Nordlund
Crystal Structure Of The Ntf2 Domain Of Ras Gtpase-Activating Protein-Binding Protein 1
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

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:121
 aligned with G3BP1_HUMAN | Q13283 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:131
                                    16        26        36        46        56        66        76        86        96       106       116       126       136 
          G3BP1_HUMAN     7 SPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEV 137
               SCOP domains d3q90a_ A: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee----------...eehhhhhhhhhhhh.....eeeeeeeeeee.hhh.eeeeeeeeee......eeeeeeeeeee.......eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----NTF2_DOMAIN  PDB: A:11-133 UniProt: 11-133                                                                                 ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q90 A   7 SPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYV----------ADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEV 137
                                    16        26        36    |    -     |  56        66        76        86        96       106       116       126       136 
                                                             41         52

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with G3BP1_HUMAN | Q13283 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:140
                             1                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139
          G3BP1_HUMAN     - -MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFG 139
               SCOP domains d3q90b_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------NTF2-3q90B01 B:11-133                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) -----------NTF2-3q90B02 B:11-133                                                                                                      ------ Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....----....eehhhhhhhhhhhh.....eeeeeeeeeee.....eeeeeeeeee......eeeeeeeeee..------.eeeeeeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------NTF2_DOMAIN  PDB: B:11-133 UniProt: 11-133                                                                                 ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q90 B   0 SMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLD----PADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPE------FYVHNDIFRYQDEVFG 139
                                     9        19        29        39      |  - |      59        69        79        89        99       109       | -    |  129       139
                                                                         46   51                                                               117    124

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (G3BP1_HUMAN | Q13283)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004003	ATP-dependent DNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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).
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0090090	negative regulation of canonical Wnt signaling pathway	Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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	3q90
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	G3BP1_HUMAN \| Q13283
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	3.6.4.12
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	3.6.4.13
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