1ZO1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   IF2, IF1, AND TRNA FITTED TO CRYO-EM DATA OF E. COLI 70S INITIATION COMPLEX

Authors :   G. S. Allen, A. Zavialov, R. Gursky, M. Ehrenberg, J. Frank

Date :   12 May 05 (Deposition) - 14 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   13.80

Chains :   Asym./Biol. Unit : F,I,W

Keywords :   E. Coli, Ribosome, Initiation Of Protein Synthesis, Initiation Factor, Cryo-Eletron Microscopy, Translation/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. S. Allen, A. Zavialov, R. Gursky, M. Ehrenberg, J. Frank
The Cryo-Em Structure Of A Translation Initiation Complex From Escherichia Coli.
Cell(Cambridge, Mass. ) V. 121 703 2005
PubMed-ID: 15935757 | Reference-DOI: 10.1016/J.CELL.2005.03.023
(for further references see the PDB file header)

Molecule 1 - P/I-SITE TRNA
	Chains	:	F
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - TRANSLATION INITIATION FACTOR 2
	Chains	:	I
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	IF2

Molecule 3 - TRANSLATION INITIATION FACTOR 1
	Chains	:	W
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	IF1

		1	2	3
Asymmetric/Biological Unit	:	F	I	W

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZO1)

(no "Site" information available for 1ZO1)

(no "SS Bond" information available for 1ZO1)

(no "Cis Peptide Bond" information available for 1ZO1)

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IF2_ECOLI_001 *	D	409	E	IF2_ECOLI	---	---	I	E	245	E
2	UniProt	VAR_IF2_ECOLI_002 *	H	432	Q	IF2_ECOLI	---	---	I	H	268	Q
3	UniProt	VAR_IF2_ECOLI_003 *	Q	490	G	IF2_ECOLI	---	---	I	Q	326	G
4	UniProt	VAR_IF2_ECOLI_004 *	G	684	A	IF2_ECOLI	---	---	I	G	520	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IF2	PS01176	Initiation factor 2 signature.	IF2_ECOLI	840-862	1	I:676-698

(no "Exon" information available for 1ZO1)

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 F from PDB  Type:RNA  Length:76
                                                                                                            
                 1zo1 F   1 GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA  76
                                    10        20        30        40        50        60        70

Chain I from PDB  Type:PROTEIN  Length:501
 aligned with IF2_ECOLI | P0A705 from UniProtKB/Swiss-Prot  Length:890

    Alignment length:501
                                   397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887 
            IF2_ECOLI   388 EPRAPVVTIMGHVDHGKTSLLDYIRSTKVASGEAGGITQHIGAYHVETENGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYRQGKFREVKLARQQKSKLENMFANMTEGEVHEVNIVLKADVQGSVEAISDSLLKLSTDEVKVKIIGSGVGGITETDATLAAASNAILVGFNVRADASARKVIEAESLDLRYYSVIYNLIDEVKAAMSGMLSPELKQQIIGLAEVRDVFKSPKFGAIAGCMVTEGVVKRHNPIRVLRDNVVIYEGELESLRRFKDDVNEVRNGMECGIGVKNYNDVRTGDVIEVFEIIEIQRT 888
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -GTP_EFTU-1zo1I01 I:225-390                                                                                                                                            ---------------------------------------------------------------------------------------------------------------------IF-2-1zo1I04 I:508-616                                                                                       -----------------------------GTP_EFTU_D2-1zo1I02 I:646-714                                        ---------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_EFTU_D2-1zo1I03 I:646-714                                        ---------- Pfam domains (2)
         Sec.struct. author ......eeeee.....hhhhhhhhhhhhhh........................ee.....................eeeeee........hhhhhhhhhhh...eeeeee..............................eeee..........hhhhhh.................eeeeeeeee.....eeeeeeeee.......eeeee....eeeee.......eeee........eee.......eeeeee..................hhhhhhhhhhhhh.....................hhhhhhhhhhhhh..................hhhhhh...hhhhh.eee.....hhhhhh........eee....hhhhhhhhhhhh..............eeeee.........eeeeeeeeeeee...eee........eeee...eee..eee.eee....eeee...........eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------E----------------------Q---------------------------------------------------------G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IF2  PDB: I:676-698    -------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zo1 I 224 EPRAPVVTIMGHVDHGKTSLLEYIRSTKVASGEAGGITQHIGAYHVETENGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYRQGKFREVKLARQQKSKLENMFANMTEGEVHEVNIVLKADVQGSVEAISDSLLKLSTDEVKVKIIGSGVGGITETDATLAAASNAILVGFNVRADASARKVIEAESLDLRYYSVIYNLIDEVKAAMSGMLSPELKQQIIGLAEVRDVFKSPKFGAIAGCMVTEGVVKRHNPIRVLRDNVVIYEGELESLRRFKDDVNEVRNGMECGIGVKNYNDVRTGDVIEVFEIIEIQRT 724
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723

Chain W from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains d1zo1w1 W:1-71 Translational initiation factor 1, IF1                   SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee...ee...ee..ee........eehhhhhhh........eee...........ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 1zo1 W   1 AKEKDTIRTEGVVTEALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYRK  71
                                    10        20        30        40        50        60        70

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Cold shock DNA-binding domain-like (310)

Protein domain: Translational initiation factor 1, IF1 (3)

Escherichia coli [TaxId: 562] (3)

d1zo1w1

W:1-71

(no "CATH Domain" information available for 1ZO1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: GTP_EFTU (39)

Escherichia coli (strain K12) (2)

GTP_EFTU-1zo1I01

I:225-390

Clan: no clan defined [family: GTP_EFTU_D2] (39)

Family: GTP_EFTU_D2 (39)

Escherichia coli (strain K12) (2)

2a	GTP_EFTU_D2-1zo1I02	I:646-714
2b	GTP_EFTU_D2-1zo1I03	I:646-714

Clan: no clan defined [family: IF-2] (2)

Family: IF-2 (2)

Escherichia coli (strain K12) (1)

IF-2-1zo1I04

I:508-616

Asymmetric/Biological Unit(hide GO term definitions)

Chain I (IF2_ECOLI | P0A705)

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:0097216	guanosine tetraphosphate binding	Interacting selectively and non-covalently with guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions.
	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:0043024	ribosomal small subunit binding	Interacting selectively and non-covalently with any part of the small ribosomal subunit.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1zo1
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	IF2_ECOLI \| P0A705
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UniProtKB/Swiss-Prot
	IF1_ECOLI \| P69222	:	1ah9
	IF2_ECOLI \| P0A705	:	1nd9 3jcj 3jcn 5me0 5me1

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

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Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (16, 22)

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