3T5G - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF FULLY MODIFIED FARNESYLATED RHEB IN COMPLEX WITH PDE6D

Authors :   S. A. Ismail, Y. -X. Chen, A. Wittinghofer

Date :   27 Jul 11 (Deposition) - 26 Oct 11 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Immunoglobulin-Like Beta Sandwitch, Pde Delta, Rheb, Farnesyl, Signaling Protein, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Ismail, Y. X. Chen, A. Rusinova, A. Chandra, M. Bierbaum, L. Gremer, G. Triola, H. Waldmann, P. I. Bastiaens, A. Wittinghofer
Arl2-Gtp And Arl3-Gtp Regulate A Gdi-Like Transport System For Farnesylated Cargo.
Nat. Chem. Biol. V. 7 942 2011
PubMed-ID: 22002721 | Reference-DOI: 10.1038/NCHEMBIO.686

Molecule 1 - GTP-BINDING PROTEIN RHEB
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RHEB, RHEB2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RAS HOMOLOG ENRICHED IN BRAIN

Molecule 2 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PDE6D, PDED
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GMP-PDE DELTA, PROTEIN P17

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CMT	1	Mod. Amino Acid	O-METHYLCYSTEINE
2	FAR	1	Ligand/Ion	FARNESYL
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:16 , VAL A:17 , GLY A:18 , LYS A:19 , SER A:20 , SER A:21 , PHE A:31 , ASN A:119 , LYS A:120 , ASP A:122 , LEU A:123 , SER A:149 , ALA A:150 , LYS A:151 , HOH A:197 , MG A:202 , HOH A:212 , HOH A:288 , HOH A:294 , HOH A:298 , HOH A:304 , HOH A:362 , HOH A:395 , HOH A:434 , HOH A:449	BINDING SITE FOR RESIDUE GDP A 201
2	AC2	SOFTWARE	SER A:20 , GDP A:201 , HOH A:395 , HOH A:396 , HOH A:434 , HOH A:449	BINDING SITE FOR RESIDUE MG A 202
3	AC3	SOFTWARE	SER A:180 , CMT A:181 , MET B:20 , LEU B:38 , ILE B:53 , GLN B:78 , TYR B:149	BINDING SITE FOR RESIDUE FAR A 2010

(no "SS Bond" information available for 3T5G)

(no "Cis Peptide Bond" information available for 3T5G)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036310	E	139	K	RHEB_HUMAN	Unclassified	---	A	E	139	K

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RHEB_HUMAN	2-184	1	A:2-181

Asymmetric/Biological Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000262187	1b	ENSE00001200523	chr7:151217010-151216546	465	RHEB_HUMAN	1-18	18	1	A:2-18	17
1.5	ENST00000262187	5	ENSE00000730260	chr7:151188100-151188029	72	RHEB_HUMAN	18-42	25	1	A:18-42	25
1.6	ENST00000262187	6	ENSE00000909920	chr7:151181890-151181823	68	RHEB_HUMAN	42-64	23	1	A:42-64	23
1.7	ENST00000262187	7	ENSE00000730253	chr7:151174501-151174419	83	RHEB_HUMAN	65-92	28	1	A:65-92	28
1.8c	ENST00000262187	8c	ENSE00001139595	chr7:151168691-151168635	57	RHEB_HUMAN	92-111	20	1	A:92-107	16
1.8f	ENST00000262187	8f	ENSE00001200505	chr7:151168527-151168480	48	RHEB_HUMAN	111-127	17	1	A:112-127	16
1.9a	ENST00000262187	9a	ENSE00001315618	chr7:151167738-151167657	82	RHEB_HUMAN	127-154	28	1	A:127-154	28
1.10d	ENST00000262187	10d	ENSE00001321653	chr7:151164297-151163098	1200	RHEB_HUMAN	155-184	30	1	A:155-181 (gaps)	27

2.3a	ENST00000287600	3a	ENSE00001829481	chr2:232646019-232645775	245	PDE6D_HUMAN	1-17	17	1	B:4-17	14
2.5b	ENST00000287600	5b	ENSE00001029423	chr2:232603898-232603810	89	PDE6D_HUMAN	17-47	31	1	B:17-47	31
2.6a	ENST00000287600	6a	ENSE00001029425	chr2:232602848-232602723	126	PDE6D_HUMAN	47-89	43	1	B:47-89	43
2.7	ENST00000287600	7	ENSE00001029421	chr2:232602002-232601897	106	PDE6D_HUMAN	89-124	36	1	B:89-124	36
2.9b	ENST00000287600	9b	ENSE00001872609	chr2:232597743-232597135	609	PDE6D_HUMAN	124-150	27	1	B:124-150	27

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:171
 aligned with RHEB_HUMAN | Q15382 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           RHEB_HUMAN     2 PQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKMDGAASQGKSSC 181
               SCOP domains d3t5ga_ A: GTP-binding protein RheB                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee..........hhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh----..eeeeee..........hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhh.-----...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------ SAPs(SNPs)
                    PROSITE RAS  PDB: A:2-181 UniProt: 2-184                                                                                                                                                     PROSITE
           Transcript 1 (1) Exon 1.1b        -----------------------Exon 1.6  PDB: A:42-64 Exon 1.7  PDB: A:65-92      ------------------Exon 1.8f        ---------------------------Exon 1.10d UniProt: 155-184 Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.5  PDB: A:18-42   -------------------------------------------------Exon 1.8c           ---------------Exon 1.9a  PDB: A:127-154   --------------------------- Transcript 1 (2)
                 3t5g A   2 PQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMV----IPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKM-----QGKSSc 181
                                    11        21        31        41        51        61        71        81        91       101     |   -|      121       131       141       151       161        |-    |  181
                                                                                                                                   107  112                                                       170   176    |
                                                                                                                                                                                                             181-CMT

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with PDE6D_HUMAN | O43924 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       
          PDE6D_HUMAN     4 KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
               SCOP domains d3t5gb_ B: GMP-PDE delta                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.3a     -----------------------------Exon 2.6a  PDB: B:47-89 UniProt: 47-89     ----------------------------------Exon 2.9b  PDB: B:124-150   Transcript 2 (1)
           Transcript 2 (2) -------------Exon 2.5b  PDB: B:17-47        -----------------------------------------Exon 2.7  PDB: B:89-124             -------------------------- Transcript 2 (2)
                 3t5g B   4 KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

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 '\|'

(no "CATH Domain" information available for 3T5G)

(no "Pfam Domain" information available for 3T5G)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RHEB_HUMAN | Q15382)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	GO:0032008	positive regulation of TOR signaling	Any process that activates or increases the frequency, rate or extent of TOR signaling.
	GO:0048714	positive regulation of oligodendrocyte differentiation	Any process that activates or increases the frequency, rate or extent of oligodendrocyte differentiation.
	GO:0032006	regulation of TOR signaling	Any process that modulates the frequency, rate or extent of TOR signaling.
	GO:2000074	regulation of type B pancreatic cell development	Any process that modulates the frequency, rate or extent of pancreatic B cell development.
	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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

Chain B (PDE6D_HUMAN | O43924)

molecular function
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0005095	GTPase inhibitor activity	Stops, prevents or reduces the activity of any enzyme that catalyzes the hydrolysis of GTP to GDP and orthophosphate.
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	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:0034260	negative regulation of GTPase activity	Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
	GO:0050896	response to stimulus	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. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	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.

Asymmetric/Biological Unit
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	RHEB_HUMAN \| Q15382
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (13, 13)

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SCOP Domains (2, 2)

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