2CLS - JenaLib

Title :   THE CRYSTAL STRUCTURE OF THE HUMAN RND1 GTPASE IN THE ACTIVE GTP BOUND STATE

Authors :   A. C. W. Pike, X. Yang, S. Colebrook, O. Gileadi, F. Sobott, J. Bray, L. We B. Marsden, Y. Zhao, G. Schoch, J. Elkins, J. E. Debreczeni, A. P. Turnb F. Von Delft, C. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, D.

Date :   28 Apr 06 (Deposition) - 04 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Nucleotide-Binding, Gtp-Binding Protein Rho6, Membrane, Prenylation, Lipoprotein, Gtp-Binding, Cytoskeleton, Small Gtpase, Nucleotide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. W. Pike, X. Yang, S. Colebrook, O. Gileadi, F. Sobott, J. Bray, L. Wen Hwa, B. Marsden, Y. Zhao, G. Schoch, J. Elkins, J. E. Debreczeni A. P. Turnbull, F. Von Delft, C. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, D. Doyle
The Crystal Structure Of The Human Rnd1 Gtpase In The Active Gtp Bound State
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:27 , THR A:45 , GTP A:500 , HOH A:2023 , HOH A:2078	BINDING SITE FOR RESIDUE MG A 550
2	AC2	SOFTWARE	THR B:27 , THR B:45 , GTP B:500 , HOH B:2012 , HOH B:2048	BINDING SITE FOR RESIDUE MG B 550
3	AC3	SOFTWARE	VAL A:22 , GLN A:23 , CYS A:24 , GLY A:25 , LYS A:26 , THR A:27 , ALA A:28 , TYR A:38 , PRO A:39 , GLU A:40 , THR A:41 , TYR A:42 , THR A:45 , SER A:69 , GLY A:70 , LYS A:126 , ASP A:128 , LEU A:129 , SER A:168 , ALA A:169 , PHE A:170 , MG A:550 , HOH A:2004 , HOH A:2023 , HOH A:2026 , HOH A:2078 , HOH A:2079 , HOH A:2080	BINDING SITE FOR RESIDUE GTP A 500
4	AC4	SOFTWARE	VAL B:22 , GLN B:23 , CYS B:24 , GLY B:25 , LYS B:26 , THR B:27 , ALA B:28 , TYR B:38 , PRO B:39 , GLU B:40 , THR B:41 , TYR B:42 , THR B:45 , SER B:69 , GLY B:70 , LYS B:126 , ASP B:128 , LEU B:129 , SER B:168 , ALA B:169 , PHE B:170 , MG B:550 , HOH B:2003 , HOH B:2012 , HOH B:2014 , HOH B:2047 , HOH B:2048 , HOH B:2049	BINDING SITE FOR RESIDUE GTP B 500

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (5, 10)

Sequences/Alignments

Asymmetric 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:179
 aligned with RND1_HUMAN | Q92730 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:179
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179         
           RND1_HUMAN    10 VVARCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCL 188
               SCOP domains d2clsa_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 2clsA00 A:10-188 P-loop containing nucleotide triphosphate hydrolases                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhh..........eeeeeeeee....eeeeeeeee..hhhhh.hhhhhhh...eeeeeee........hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:10-40         Exon 1.2  PDB: A:41-70        ------------------------------------Exon 1.4  PDB: A:107-151 UniProt: 107-151    Exon 1.5  PDB: A:152-188 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.3  PDB: A:70-106              ---------------------------------------------------------------------------------- Transcript 1 (2)
                 2cls A  10 VVARCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCL 188
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with RND1_HUMAN | Q92730 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
           RND1_HUMAN    11 VARCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCL 188
               SCOP domains d2clsb_ B: automated matches                                                                                                                                                       SCOP domains
               CATH domains 2clsB00 B:11-188 P-loop containing nucleotide triphosphate hydrolases                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeee....eeeeeeeee..hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:11-40        Exon 1.2  PDB: B:41-70        ------------------------------------Exon 1.4  PDB: B:107-151 UniProt: 107-151    Exon 1.5  PDB: B:152-188 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.3  PDB: B:70-106              ---------------------------------------------------------------------------------- Transcript 1 (2)
                 2cls B  11 VARCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCL 188
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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 (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RND1_HUMAN | Q92730)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0007015	actin filament organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0007162	negative regulation of cell adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
	GO:0016322	neuron remodeling	The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
	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:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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: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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