1QZD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME

Authors :   M. Valle, A. Zavialov, W. Li, S. M. Stagg, J. Sengupta, R. C. Nielsen, P. Nissen, S. C. Harvey, M. Ehrenberg, J. Frank

Date :   16 Sep 03 (Deposition) - 04 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   10.00

Chains :   Asym./Biol. Unit : A

Keywords :   Elongation Factor, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Valle, A. Zavialov, W. Li, S. M. Stagg, J. Sengupta, R. C. Nielsen, P. Nissen, S. C. Harvey, M. Ehrenberg, J. Frank
Incorporation Of Aminoacyl-Trna Into The Ribosome As Seen By Cryo-Electron Microscopy
Nat. Struct. Biol. V. 10 899 2003
PubMed-ID: 14566331 | Reference-DOI: 10.1038/NSB1003
(for further references see the PDB file header)

Molecule 1 - ELONGATION FACTOR TU
	Chains	:	A
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	EF-TU, P-43

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1QZD)

(no "Site" information available for 1QZD)

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

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

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

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.	EFTU1_ECOLI	51-66	1	A:50-65
1	G_TR_1	PS00301		EFTU2_ECOLI	51-66	1	A:50-65

(no "Exon" information available for 1QZD)

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:393
 aligned with EFTU1_ECOLI | P0CE47 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:393
                                    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       371       381       391   
          EFTU1_ECOLI     2 SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 394
               SCOP domains d1qzda_ A: 70S ribosome functional complex                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qzd A   1 SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 393
                                    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

Chain A from PDB  Type:PROTEIN  Length:393
 aligned with EFTU2_ECOLI | P0CE48 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:393
                                    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       371       381       391   
          EFTU2_ECOLI     2 SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 394
               SCOP domains d1qzda_ A: 70S ribosome functional complex                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................................................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qzd A   1 SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 393
                                    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

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Low resolution protein structures (283)

Fold: Ribosome and ribosomal fragments (154)

Superfamily: Ribosome and ribosomal fragments (154)

Family: Ribosome complexes (103)

Protein domain: 70S ribosome functional complex (103)

Escherichia coli [TaxId: 562] (72)

d1qzda_

(no "CATH Domain" information available for 1QZD)

(no "Pfam Domain" information available for 1QZD)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (EFTU1_ECOLI | P0CE47)

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:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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: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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (EFTU2_ECOLI | P0CE48)

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:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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: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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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1ob2	E. COLI ELONGATION FACTOR EF-TU COMPLEXED WITH THE ANTIBIOTIC KIRROMYCIN, A GTP ANALOG, AND PHE-TRNA
1qza	COORDINATES OF THE A/T SITE TRNA MODEL FITTED INTO THE CRYO -EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME
1qzb	COORDINATES OF THE A-SITE TRNA MODEL FITTED INTO THE CRYO- EM MAP OF 70S RIBOSOME IN THE PRE-TRANSLOCATIONAL STATE
1qzc	COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN)BOUND 70S RIBOSOME
1r2w	COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF THE 70S RIBOSOME
1r2x	COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME RELATED ID: EMD-1055 RELATED DB: EMDB

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Ligands, Modified Residues, Ions (0, 0)

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PROSITE Motifs (1, 1)

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SCOP Domains (1, 1)

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Gene Ontology (14, 27)

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