2E1R - JenaLib

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Title :   STRUCTURE OF EEF2 IN COMPLEX WITH A SORDARIN DERIVATIVE

Authors :   R. Soe, R. T. Mosley, G. R. Andersen

Date :   27 Oct 06 (Deposition) - 14 Nov 06 (Release) - 12 Aug 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.15

Chains :   Asym./Biol. Unit : A

Keywords :   Protein-Ligand Complex, G-Protein, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Soe, R. T. Mosley, M. Justice, J. Nielsen-Kahn, M. Shastry, A. R. Merrill, G. R. Andersen
Sordarin Derivatives Induce A Novel Conformation Of The Yeast Ribosome Translocation Factor Eef2
J. Biol. Chem. V. 282 657 2007
PubMed-ID: 17082187 | Reference-DOI: 10.1074/JBC.M607830200
(for further references see the PDB file header)

Molecule 1 - ELONGATION FACTOR 2
	Chains	:	A
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	EF-2, TRANSLATION ELONGATION FACTOR 2, EUKARYOTIC ELONGATION FACTOR 2, EEF2, RIBOSOMAL TRANSLOCASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	SOD	1	Ligand/Ion	(1S,4S,5S,6R,9S,11S)-6-CHLORO-9-FORMYL-13-ISOPROPYL-5-METHYL-2-({[(3AR,5R,7R ,7AS)-7-METHYL-3-METHYLENEHEXAHYDRO-2H-FURO[2,3-C]PYRAN-5-YL]OXY}METHYL)TETR ACYCLO[7.4.0.02,11.04,8]TRIDEC-12-ENE-1-CARBOXYLIC ACI

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:487 , GLN A:490 , LEU A:519 , TYR A:521 , SER A:523 , GLU A:524 , ILE A:529 , VAL A:561 , ALA A:562 , PRO A:727 , VAL A:774 , TRP A:801	BINDING SITE FOR RESIDUE SOD A 901
2	AC2	SOFTWARE	VAL A:28 , HIS A:30 , GLY A:31 , LYS A:32 , SER A:33 , THR A:34 , ASN A:158 , LYS A:159 , ASP A:161 , SER A:213 , GLY A:214 , LEU A:215	BINDING SITE FOR RESIDUE GDP A 902

(no "SS Bond" information available for 2E1R)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:637	-	Pro A:638

(no "SAP(SNP)/Variant" information available for 2E1R)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EF2_YEAST	58-73	1	A:65-73

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	YOR133W	2	YOR133W.1	XV:575099-577627	2529	EF2_YEAST	1-842	842	1	A:1-842 (gaps)	842

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:828
 aligned with EF2_YEAST | P32324 from UniProtKB/Swiss-Prot  Length:842

    Alignment length:842
                                    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       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840  
            EF2_YEAST     1 MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL 842
               SCOP domains d2e1ra2 A:1-343 automated matches                                                                                                                                                                                                                                                                                                                      d2e1ra1 A:344-481 automated matches                                                                                                       d2e1ra4 A:482-560 automated matches                                            d2e1ra3 A:561-725 automated matches                                                                                                                                  d2e1ra5 A:726-842 automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhheee...--------------.........eeeeeee................eeeeeee.........hhhhhhhh...eeeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.eeeee....eeeehhhhhhhhhhhh..hhhhhhhhh....eee....eee............hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhh.......eeeeeeee........eeeeeeee.eee.....eee...........ee.....eeeeee..eeeee.eee...eeeee.........eeee..................eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeee.....eeeee.hhhhhhhhhhhhhhh.....eeee......eeee.......eeee......eeeeeeee.hhhhhhhhhh.......hhhhhhhhhhhh...hhhhhh.eeee.......eeeee......hhhhhhhhhhhhhhhhh........ee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhhhhhhh...eeeeeee......eeeeeeee.hhh.hhhhhhhhhh.........eeeeee.........hhhhhhhhhhhhhhh......hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-842 (gaps) UniProt: 1-842                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                 2e1r A   1 MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAK--------------ERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL 842
                                    10        20        30        40        50         -    |   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       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840  
                                                                            50             65

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 2E1R)

(no "Pfam Domain" information available for 2E1R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (EF2_YEAST | P32324)

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:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:1990145	maintenance of translational fidelity	Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template.
	GO:0017183	peptidyl-diphthamide biosynthetic process from peptidyl-histidine	The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.
	GO:0045901	positive regulation of translational elongation	Any process that activates or increases the frequency, rate or extent of translational elongation.
	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.
cellular component
	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: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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	Cis Peptide Bonds
		Gly A:637 - Pro A:638	[ RasMol ]

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	2e1r
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1n0u	STRUCTURE OF EEF2 IN COMPLEX WITH SORDARIN
2npf	STRUCTURE OF EEF2 IN COMPLEX WITH MORINIAFUNGIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 5)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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