1G7T - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B COMPLEXED WITH GDPNP

Authors :   A. Roll-Mecak, C. Cao, T. E. Dever, S. K. Burley

Date :   14 Nov 00 (Deposition) - 01 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Translational Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Roll-Mecak, C. Cao, T. E. Dever, S. K. Burley
X-Ray Structures Of The Universal Translation Initiation Factor If2/Eif5B: Conformational Changes On Gdp And Gtp Binding.
Cell(Cambridge, Mass. ) V. 103 781 2000
PubMed-ID: 11114334 | Reference-DOI: 10.1016/S0092-8674(00)00181-1
(for further references see the PDB file header)

Molecule 1 - TRANSLATION INITIATION FACTOR IF2/EIF5B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	Organism Taxid	:	145262

		1
Asymmetric/Biological Unit	:	A

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	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:19 , GNP A:601 , HOH A:844	BINDING SITE FOR RESIDUE MG A 602
2	AC2	SOFTWARE	HIS A:13 , VAL A:14 , ASP A:15 , HIS A:16 , GLY A:17 , LYS A:18 , THR A:19 , THR A:20 , GLU A:81 , ASN A:130 , LYS A:131 , ASP A:133 , ARG A:134 , SER A:198 , ALA A:199 , ILE A:200 , MG A:602 , HOH A:737 , HOH A:746 , HOH A:844 , HOH A:849 , HOH A:895 , HOH A:934 , HOH A:966	BINDING SITE FOR RESIDUE GNP A 601

(no "SS Bond" information available for 1G7T)

(no "Cis Peptide Bond" information available for 1G7T)

(no "SAP(SNP)/Variant" information available for 1G7T)

(no "PROSITE Motif" information available for 1G7T)

(no "Exon" information available for 1G7T)

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
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Chain A from PDB  Type:PROTEIN  Length:569
 aligned with IF2P_METTH | O26359 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:586
                                    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       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580      
           IF2P_METTH     1 MKIRSPIVSVLGHVDHGKTTLLDHIRGSAVASREAGGITQHIGATEIPMDVIEGICGDFLKKFSIRETLPGLFFIDTPGHEAFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYRTPFVVAANKIDRIHGWRVHEGRPFMETFSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTMLMGLAQQYLREQLKIEEDSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDVISTRIRSLLKPRPLEEMRESRKKFQKVDEVVAAAGIKIVAPGIDDVMAGSPLRVVTDPEKVREEILSEIEDIKIDTDEAGVVVKADTLGSLEAVVKILRDMYVPIKVADIGDVSRRDVVNAGIALQEDRVYGAIIAFNVKVIPSAAQELKNSDIKLFQGNVIYRLMEEYEEWVRGIEEEKKKKWMEAIIKPASIRLIPKLVFRQSKPAIGGVEVLTGVIRQGYPLMNDDGETVGTVESMQDKGENLKSASRGQKVAMAIKDAVYGKTIHEGDTLYVDIPENHYHILKEQLSGDLTDEELDLMDKIAEIKRKKNP 586
               SCOP domains d1g7ta4 A:1-227 Initiation factor     IF2/eIF5b, N-terminal (G) domain                                                                                                                                                             d1g7ta1 A:228-328 Initiation factor IF2/eIF5b, domains 2 a      nd 4                                 d1g7ta3 A:329-459 Initiation factor IF2/eIF5b, domain 3                                                                            d1g7ta2 A:460-586 Initiation factor IF2/eIF5b, domains 2 and 4                                                                  SCOP domains
               CATH domains 1g7tA01 A:1-225 P-loop containing     nucleotide triphosphate hydrolases                                                                                                                                                         1g7tA02 A:226-337 Translation factors                                                                           -------------1g7tA03 A:351-431  [code=3.40.50.10050, no name defined]                         ------------------------------1g7tA04 A:462-550 Translation factors                                                    --------       --------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeeee....hhhhhhhhhhhhhhh..----..ee..eeeeehhhhhhhhhhhhh.hhhhhh..eeeeee.....hhhh.ee..ee...eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee..........eeeee.......hhhhhhhhhhhhhhhhhhhh.ee......eeeeeeeee.....eeeeeeeee.eee...eeeee....eeeee..eeeee..------....eeee.eee..eeeeee...........eeee..hhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh......eeeee....hhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee....eeeeeeeeee......eee.....eeeeeeeeee..eee........eeeeee............eeee..hhhhhhh.-------.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g7t A   1 MKIRSPIVSVLGHVDHGKTTLLDHIRGSAVASR----ITQHIGATEIPMDVIEGICGDFLKKFSIRETLPGLFFIDTPGHEAFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYRTPFVVAANKIDRIHGWRVHEGRPFMETFSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTMLMGLAQQYLREQLKIEEDSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDVISTRIRSLLKPRP------SRKKFQKVDEVVAAAGIKIVAPGIDDVMAGSPLRVVTDPEKVREEILSEIEDIKIDTDEAGVVVKADTLGSLEAVVKILRDMYVPIKVADIGDVSRRDVVNAGIALQEDRVYGAIIAFNVKVIPSAAQELKNSDIKLFQGNVIYRLMEEYEEWVRGIEEEKKKKWMEAIIKPASIRLIPKLVFRQSKPAIGGVEVLTGVIRQGYPLMNDDGETVGTVESMQDKGENLKSASRGQKVAMAIKDAVYGKTIHEGDTLYVDIPENHYHIL-------LTDEELDLMDKIAEIKRKKNP 586
                                    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    |    - |     300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       | -     | 570       580      
                                                           33   38                                                                                                                                                                                                                                                    285    292                                                                                                                                                                                                                                                                       558     566

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 "Pfam Domain" information available for 1G7T)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IF2P_METTH | O26359)

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: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: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.

Asymmetric/Biological Unit
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	IF2P_METTH \| O26359	:	1g7r 1g7s 4v8z

1g7r	X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B, APO FORM
1g7s	X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B COMPLEXED WITH GDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 4)

CATH Domains (3, 4)

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Gene Ontology (7, 7)

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