4A9A - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF RBG1 IN COMPLEX WITH TMA46 DFRP DOMAIN

Authors :   S. M. Francis, M. Gas, M. Daugeron, B. Seraphin, J. Bravo

Date :   25 Nov 11 (Deposition) - 03 Oct 12 (Release) - 25 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.67

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

Keywords :   Translation, Drg-Dfrp Complex, Ribosome Binding Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Francis, M. Gas, M. Daugeron, J. Bravo, B. Seraphin
Rbg1-Tma46 Dimer Structure Reveals New Functional Domains And Their Role In Polysome Recruitment.
Nucleic Acids Res. V. 40 11100 2012
PubMed-ID: 23002146 | Reference-DOI: 10.1093/NAR/GKS867

Molecule 1 - RIBOSOME-INTERACTING GTPASE 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CODONPLUS-RIPL
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GTP-BINDING PROTEIN RBG1, GENETICALLY INTERACTS WITH RIBOSOMAL GENES PROTEIN 1, RBG1

Molecule 2 - TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CODONPLUS-RIPL
	Expression System Vector Type	:	PLASMID
	Fragment	:	DFRP DOMAIN, RESIDUES 205-345
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	DRG FAMILY-REGULATORY PROTEIN 1, TMA46

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4A9A)

(no "Site" information available for 4A9A)

(no "SS Bond" information available for 4A9A)

Asymmetric Unit

No.	Residues
1	Gln A:348	-	Pro A:349
2	Ser B:45	-	Ala B:46
3	Gln B:348	-	Pro B:349
4	Gly D:321	-	Gly D:322

(no "SAP(SNP)/Variant" information available for 4A9A)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_OBG	PS51710	OBG-type guanine nucleotide-binding (G) domain profile.	RBG1_YEAST	66-292	2	A:66-292 B:66-292
2	GTP1_OBG	PS00905	GTP1/OBG family signature.	RBG1_YEAST	118-131	2	A:118-131 B:118-125

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_OBG	PS51710	OBG-type guanine nucleotide-binding (G) domain profile.	RBG1_YEAST	66-292	1	A:66-292 -
2	GTP1_OBG	PS00905	GTP1/OBG family signature.	RBG1_YEAST	118-131	1	A:118-131 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_OBG	PS51710	OBG-type guanine nucleotide-binding (G) domain profile.	RBG1_YEAST	66-292	1	- B:66-292
2	GTP1_OBG	PS00905	GTP1/OBG family signature.	RBG1_YEAST	118-131	1	- B:118-125

(no "Exon" information available for 4A9A)

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:356
 aligned with RBG1_YEAST | P39729 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:368
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
           RBG1_YEAST     2 STTVEKIKAIEDEMARTQKNKATSFHLGQLKAKLAKLRRELLTSASSGSGGGAGIGFDVARTGVASVGFVGFPSVGKSTLLSKLTGTESEAAEYEFTTLVTVPGVIRYKGAKIQMLDLPGIIDGAKDGRGRGKQVIAVARTCNLLFIILDVNKPLHHKQIIEKELEGVGIRLNKTPPDILIKKKEKGGISITNTVPLTHLGNDEIRAVMSEYRINSAEIAFRCDATVDDLIDVLEASSRRYMPAIYVLNKIDSLSIEELELLYRIPNAVPISSGQDWNLDELLQVMWDRLNLVRIYTKPKGQIPDFTDPVVLRSDRCSVKDFCNQIHKSLVDDFRNALVYGSSVKHQPQYVGLSHILEDEDVVTILKK 369
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.-------.............eeeeee...hhhhhhhhhhhhh...hhhhh......eeeeeeee..eeeeeee.hhhh..-----hhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh.eee......eeeee.....eeeee.......hhhhhhhhhhhh....eeeee....hhhhhhhhhh....eee.eeeeeehhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhh.eeeee............eee.....hhhhhhhhhhhhhhh.eeeeeee........eee..........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------G_OBG  PDB: A:66-292 UniProt: 66-292                                                                                                                                                                                               ----------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------GTP1_OBG      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a9a A   2 STTVEKIKAIEDEMARTQKNKATSFHLGQLKAKLAKLRRELLTS-------GAGIGFDVARTGVASVGFVGFPSVGKSTLLSKLTGTESEAAEYEFTTLVTVPGVIRYKGAKIQMLDLPGIIDG-----GRGKQVIAVARTCNLLFIILDVNKPLHHKQIIEKELEGVGIRLNKTPPDILIKKKEKGGISITNTVPLTHLGNDEIRAVMSEYRINSAEIAFRCDATVDDLIDVLEASSRRYMPAIYVLNKIDSLSIEELELLYRIPNAVPISSGQDWNLDELLQVMWDRLNLVRIYTKPKGQIPDFTDPVVLRSDRCSVKDFCNQIHKSLVDDFRNALVYGSSVKHQPQYVGLSHILEDEDVVTILKK 369
                                    11        21        31        41   |     - |      61        71        81        91       101       111       121   |   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
                                                                      45      53                                                                     125   131

Chain B from PDB  Type:PROTEIN  Length:355
 aligned with RBG1_YEAST | P39729 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:368
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
           RBG1_YEAST     2 STTVEKIKAIEDEMARTQKNKATSFHLGQLKAKLAKLRRELLTSASSGSGGGAGIGFDVARTGVASVGFVGFPSVGKSTLLSKLTGTESEAAEYEFTTLVTVPGVIRYKGAKIQMLDLPGIIDGAKDGRGRGKQVIAVARTCNLLFIILDVNKPLHHKQIIEKELEGVGIRLNKTPPDILIKKKEKGGISITNTVPLTHLGNDEIRAVMSEYRINSAEIAFRCDATVDDLIDVLEASSRRYMPAIYVLNKIDSLSIEELELLYRIPNAVPISSGQDWNLDELLQVMWDRLNLVRIYTKPKGQIPDFTDPVVLRSDRCSVKDFCNQIHKSLVDDFRNALVYGSSVKHQPQYVGLSHILEDEDVVTILKK 369
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..............hhhhhheeeeeee.....hhhhhhhhhhh....------.......eeeee..eeeeeee.hhhh..-------hhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh.eee......eeeee.....eeeee.......hhhhhhhhhhhh....eeeee....hhhhhhhhhh....eee.eeeeeehhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhheeeeee............eeee....hhhhhhhhhh.hhhhhh.eeeee........eee.........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------G_OBG  PDB: B:66-292 UniProt: 66-292                                                                                                                                                                                               ----------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------GTP1_OBG      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a9a B   2 STTVEKIKAIEDEMARTQKNKATSFHLGQLKAKLAKLRRELLTSASSGSGGGAGIGFDVARTGVASVGFVGFPSVGKSTLLSKLTGTESE------TTLVTVPGVIRYKGAKIQMLDLPGIIDG-------GKQVIAVARTCNLLFIILDVNKPLHHKQIIEKELEGVGIRLNKTPPDILIKKKEKGGISITNTVPLTHLGNDEIRAVMSEYRINSAEIAFRCDATVDDLIDVLEASSRRYMPAIYVLNKIDSLSIEELELLYRIPNAVPISSGQDWNLDELLQVMWDRLNLVRIYTKPKGQIPDFTDPVVLRSDRCSVKDFCNQIHKSLVDDFRNALVYGSSVKHQPQYVGLSHILEDEDVVTILKK 369
                                    11        21        31        41        51        61        71        81        91      |101       111       121   |     - |     141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361        
                                                                                                                    91     98                        125     133

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with TMA46_YEAST | Q12000 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:125
                                   223       233       243       253       263       273       283       293       303       313       323       333     
          TMA46_YEAST   214 LEKQPKITLEEFIETERGKLDKSKLTPITIANFAQWKKDHVIAKINAEKKLSSKRKPTGREIILKMSAENKSFETDNADMPDDVTQGSAWDLTEFTDALKKADHQDDGGIKDYGDGSNPTFDIKK 338
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh-------------------...hhhhhhhhhhhhhhhhhhhee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a9a C 214 LEKQPKITLEEFIETERGKLDKSKLTPITIANFAQWKKDHVIAKINAEKKLSSKRKPTGREIILKMSAE-------------------AWDLTEFTDALKKADHQDDGGIKDYGDGSNPTFDIKK 338
                                   223       233       243       253       263       273        |-         -       303       313       323       333     
                                                                                              282                 302

Chain D from PDB  Type:PROTEIN  Length:86
 aligned with TMA46_YEAST | Q12000 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:123
                                   223       233       243       253       263       273       283       293       303       313       323       333   
          TMA46_YEAST   214 LEKQPKITLEEFIETERGKLDKSKLTPITIANFAQWKKDHVIAKINAEKKLSSKRKPTGREIILKMSAENKSFETDNADMPDDVTQGSAWDLTEFTDALKKADHQDDGGIKDYGDGSNPTFDI 336
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.-------------------------------------....ee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a9a D 214 LEKQPKITLEEFIETERGKLDKSKLTPITIANFAQWKKDHVIAKINAEKKLSSKRKPTGREIILKMSAE-------------------------------------DGGIKDYGDGSNPTFDI 336
                                   223       233       243       253       263       273        |-         -         -         -      |323       333   
                                                                                              282                                   320

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 4A9A)

(no "CATH Domain" information available for 4A9A)

(no "Pfam Domain" information available for 4A9A)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RBG1_YEAST | P39729)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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:0002181	cytoplasmic translation	The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
	GO:1903833	positive regulation of cellular response to amino acid starvation	Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0042788	polysomal ribosome	A ribosome bound to mRNA that forms part of a polysome.
	GO:0005844	polysome	A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

Chain C,D (TMA46_YEAST | Q12000)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0002181	cytoplasmic translation	The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the 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:0042788	polysomal ribosome	A ribosome bound to mRNA that forms part of a polysome.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4a9a)

	Sites
(no "Sites" information available for 4a9a)

	Cis Peptide Bonds
		Gln A:348 - Pro A:349	[ RasMol ]
		Gln B:348 - Pro B:349	[ RasMol ]
		Gly D:321 - Gly D:322	[ RasMol ]
		Ser B:45 - Ala B:46	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4a9a
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	RBG1_YEAST \| P39729
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	TMA46_YEAST \| Q12000
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(no "Entries Sharing at Least One Protein Chain" available for 4A9A)

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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