3RFG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE YEAST RACK1 DIMER IN SPACE GROUP P63

Authors :   L. Yatime, K. L. Hein, J. Nilsson, P. Nissen

Date :   06 Apr 11 (Deposition) - 06 Jul 11 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.90

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

Keywords :   Beta-Propeller, Dimer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Yatime, K. L. Hein, J. Nilsson, P. Nissen
Structure Of The Rack1 Dimer From Saccharomyces Cerevisiae
J. Mol. Biol. V. 411 486 2011
PubMed-ID: 21704636 | Reference-DOI: 10.1016/J.JMB.2011.06.017

Molecule 1 - GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET46 EK/LIC
	Expression System Strain	:	C43(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ASC1, CPC2, YM9718.15C, YMR116C
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C
	Synonym	:	RECEPTOR FOR ACTIVATED C KINASE, RECEPTOR OF ACTIVATED PROTEIN KINASE C 1, RACK1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3RFG)

(no "Site" information available for 3RFG)

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

Asymmetric/Biological Unit

No.	Residues
1	Asp A:266	-	Pro A:267
2	Asp B:266	-	Pro B:267

(no "SAP(SNP)/Variant" information available for 3RFG)

Asymmetric/Biological Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WD_REPEATS_1	PS00678	Trp-Asp (WD) repeats signature.	GBLP_YEAST	80-94 169-183 211-225	6	A:80-94 B:80-94 A:182-183 B:182-183 A:211-225 B:211-225

Asymmetric/Biological Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YMR116C	1	YMR116C.1	XIII:500687-500151	537	GBLP_YEAST	1-179	179	2	A:6-157 B:6-157	152 152
1.2	YMR116C	2	YMR116C.2	XIII:499877-499455	423	GBLP_YEAST	180-319	140	2	A:182-317 B:182-317	136 136

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:288
 aligned with GBLP_YEAST | P38011 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:312
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315  
           GBLP_YEAST     6 VLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMT 317
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.......eeee......eeeee.....eeeeee.......eeeeeee......eeeeee.....eeeeee....eeeee................eee........eeeeee....eeeee....eee.......eeeeeee.------------------------...eeeeeeeeee.......eee.....eeeee....eeeeee.........ee....eeee.......eeeeee...eeeee.....eeeee..............eeeeee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------WD_REPEATS_1   ---------------------------WD_REPEATS_1   -------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:6-157 UniProt: 1-179 [INCOMPLETE]                                                                                                                            Exon 1.2  PDB: A:182-317 UniProt: 180-319 [INCOMPLETE]                                                                                     Transcript 1
                 3rfg A   6 VLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVV------------------------NLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMT 317
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 |       -         -      |185       195       205       215       225       235       245       255       265       275       285       295       305       315  
                                                                                                                                                                                 157                      182

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with GBLP_YEAST | P38011 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:312
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315  
           GBLP_YEAST     6 VLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMT 317
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB01 B:290-314   --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB02 B:290-314   --- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB03 B:290-314   --- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB04 B:290-314   --- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB05 B:290-314   --- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB06 B:290-314   --- Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB07 B:290-314   --- Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB08 B:290-314   --- Pfam domains (8)
           Pfam domains (9) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB09 B:290-314   --- Pfam domains (9)
          Pfam domains (10) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB10 B:290-314   --- Pfam domains (10)
          Pfam domains (11) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB11 B:290-314   --- Pfam domains (11)
          Pfam domains (12) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-3rfgB12 B:290-314   --- Pfam domains (12)
         Sec.struct. author .eeeeeeee.......eeee......eeeee.....eeeeee.......eeeeeee......eeeeee.....eeeeee....eeeee................eee........eeeeee....eeeee....eee.......eeeeeee.------------------------...eeeeeeeeee.......eee.....eeeee....eeeeee.........ee....eeee.......eeeeee...eeeee.....eeeee..............eeeeee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------WD_REPEATS_1   ---------------------------WD_REPEATS_1   -------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:6-157 UniProt: 1-179 [INCOMPLETE]                                                                                                                            Exon 1.2  PDB: B:182-317 UniProt: 180-319 [INCOMPLETE]                                                                                     Transcript 1
                 3rfg B   6 VLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVV------------------------NLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMT 317
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 |       -         -      |185       195       205       215       225       235       245       255       265       275       285       295       305       315  
                                                                                                                                                                                 157                      182

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 "SCOP Domain" information available for 3RFG)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta_propeller (192)

Family: WD40 (64)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (18)

1a	WD40-3rfgB01	B:290-314
1b	WD40-3rfgB02	B:290-314
1c	WD40-3rfgB03	B:290-314
1d	WD40-3rfgB04	B:290-314
1e	WD40-3rfgB05	B:290-314
1f	WD40-3rfgB06	B:290-314
1g	WD40-3rfgB07	B:290-314
1h	WD40-3rfgB08	B:290-314
1i	WD40-3rfgB09	B:290-314
1j	WD40-3rfgB10	B:290-314
1k	WD40-3rfgB11	B:290-314
1l	WD40-3rfgB12	B:290-314

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GBLP_YEAST | P38011)

molecular function
	GO:0001965	G-protein alpha-subunit binding	Interacting selectively and non-covalently with a G-protein alpha subunit. The alpha subunit binds a guanine nucleotide.
	GO:0005092	GDP-dissociation inhibitor activity	Prevents the dissociation of GDP from a GTPase, thereby preventing GTP from binding.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0010255	glucose mediated signaling pathway	The process in which a change in the level of mono- and disaccharide glucose trigger the expression of genes controlling metabolic and developmental processes.
	GO:0001403	invasive growth in response to glucose limitation	A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:2001125	negative regulation of translational frameshifting	Any process that stops, prevents or reduces the frequency, rate or extent of translational frameshifting.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0022627	cytosolic small ribosomal subunit	The small subunit of a ribosome located in the cytosol.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3rfg)

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(no "Sites" information available for 3rfg)

	Cis Peptide Bonds
		Asp A:266 - Pro A:267	[ RasMol ]
		Asp B:266 - Pro B:267	[ RasMol ]

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	3rfg
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (2, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (1, 12)

Gene Ontology (11, 11)

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