3KKP - JenaLib

Title :   CRYSTAL STRUCTURE OF M-RAS P40D IN COMPLEX WITH GPPNHP

Authors :   S. Muraoka, F. Shima, J. Liao, Y. Ijiri, K. Matsumoto, M. Ye, T. Inoue, T.

Date :   06 Nov 09 (Deposition) - 16 Jun 10 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A

Keywords :   Gtp-Binding, Gtpase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Shima, Y. Ijiri, S. Muraoka, J. Liao, M. Ye, M. Araki, K. Matsumoto, N. Yamamoto, T. Sugimoto, Y. Yoshikawa, T. Kumasaka, M. Yamamoto, A. Tamura, T. Kataoka
Structural Basis For Conformational Dynamics Of Gtp-Bound Ras Protein
J. Biol. Chem. V. 285 22696 2010
PubMed-ID: 20479006 | Reference-DOI: 10.1074/JBC.M110.125161

Compounds

Molecule 1 - RAS-RELATED PROTEIN M-RAS
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	AG-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	G DOMAIN, UNP RESIDUES 1-178
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	RAS-RELATED PROTEIN R-RAS3, MUSCLE AND MICROSPIKES RAS, X- RAS

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:22 , GLY A:23 , VAL A:24 , GLY A:25 , LYS A:26 , SER A:27 , ALA A:28 , PHE A:38 , ASP A:40 , GLY A:70 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , LYS A:135 , SER A:156 , ALA A:157 , LYS A:158 , MG A:180 , HOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1010 , HOH A:1015 , HOH A:1032 , HOH A:1037 , HOH A:1138	BINDING SITE FOR RESIDUE GNP A 179
2	AC2	SOFTWARE	SER A:27 , GNP A:179 , HOH A:1001 , HOH A:1002 , HOH A:1003	BINDING SITE FOR RESIDUE MG A 180

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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:168
 aligned with RASM_MOUSE | O08989 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:168
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           RASM_MOUSE    11 LPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
               SCOP domains d3kkpa_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains 3kkpA00 A:11-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                    CATH domains
               Pfam domains ----Ras-3kkpA01 A:15-177                                                                                                                                               - Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh.hhhhhhhhhh..eeeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kkp A  11 LPTYKLVVVGDGGVGKSALTIQFFQKIFVDDYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RASM_MOUSE | O08989)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0030742	GTP-dependent 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) using energy from the hydrolysis of GTP.
	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.
biological process
	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:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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: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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	Sites
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	Cis Peptide Bonds
		Asp A:159 - Pro A:160	[ RasMol ]

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