3QSY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RECOGNITION OF THE METHIONYLATED INITIATOR TRNA BY THE TRANSLATION INITIATION FACTOR 2 IN ARCHAEA

Authors :   O. S. Nikonov, E. A. Stolboushkina, N. V. Zelinskaya, A. D. Nikulin, M. B S. V. Nikonov

Date :   22 Feb 11 (Deposition) - 21 Mar 12 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Translation Initiation, Archaea, E/Aif2, Trnai, G-Protein, Gtp Binding, Met-Trnai Binding, Ribosome Binding, Mrna Binding, Ribosome, Translation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Stolboushkina, S. Nikonov, N. Zelinskaya, V. Arkhipova, A. Nikulin, M. Garber, O. Nikonov
Crystal Structure Of The Archaeal Translation Initiation Factor 2 In Complex With A Gtp Analogue And Met-Trnaf(Met. )
J. Mol. Biol. V. 425 989 2013
PubMed-ID: 23291527 | Reference-DOI: 10.1016/J.JMB.2012.12.023

Molecule 1 - TRANSLATION INITIATION FACTOR 2 SUBUNIT GAMMA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	EIF2G
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	AIF2-GAMMA, EIF-2-GAMMA

Molecule 2 - TRANSLATION INITIATION FACTOR 2 SUBUNIT ALPHA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	DOMAIN 3
	Gene	:	EIF2A
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	AIF2-ALPHA, EIF-2-ALPHA

Molecule 3 - TRNA
	Chains	:	D
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	MET-TRNAI FROM ESCHERICHIA COLI(UNMODIFIED BASES)

		1	2	3
Asymmetric/Biological Unit	:	A	B	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MET	1	Mod. Amino Acid	METHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:18 , ASP A:19 , HIS A:20 , GLY A:21 , LYS A:22 , THR A:23 , ASN A:121 , LYS A:150	BINDING SITE FOR RESIDUE GNP A 501
2	AC2	SOFTWARE	ARG A:130 , A D:76	BINDING SITE FOR RESIDUE MET D 77

Asymmetric/Biological Unit

No.	Residues
1	A:59	-	A:74
2	A:62	-	A:77

Asymmetric/Biological Unit

No.	Residues
1	Leu A:256	-	Pro A:257

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

(no "PROSITE Motif" information available for 3QSY)

(no "Exon" information available for 3QSY)

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:415
 aligned with IF2G_SULSO | Q980A5 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:415
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410     
           IF2G_SULSO     1 MAWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.......hhhhhh.............................ee.........................ee.....eee........hhhhhhh........ee.......hhhhhhhhhhhh.........ee........hhhhhhhhhhhhhh..........ee........hhhhhhhhh......................................................eeeeee..........eeee........................................................eeee......................eeeee.....eeeeeeee...eeeeee............eeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qsy A   1 MAWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with IF2A_SULSO | Q97Z79 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:89
                                   185       195       205       215       225       235       245       255         
           IF2A_SULSO   176 KVKMSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEENVDISVV 264
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.ee...hhhhhhhhhhhhh...hhhhh..eeeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 3qsy B 176 KVKMSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEENVDISVV 264
                                   185       195       205       215       225       235       245       255

Chain D from PDB  Type:RNA  Length:77
                                                                                                             
                 3qsy D   1 CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA  76
                                    10       |19        29        39        49        59        69       
                                           17A

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 3QSY)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IF2G_SULSO | Q980A5)

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:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0001731	formation of translation preinitiation complex	The joining of the small ribosomal subunit, ternary complex, and mRNA.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	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.

Chain B (IF2A_SULSO | Q97Z79)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	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/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:256 - Pro A:257	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3QSY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (14, 17)

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