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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYO-EM OF A PRE-RECYCLING COMPLEX WITH ERF1 AND ABCE1

Authors :   A. Preis, A. Heuer, C. Barrio-Garcia, A. Hauser, D. Eyler, O. Berningha R. Green, T. Becker, R. Beckmann

Date :   28 Feb 14 (Deposition) - 23 Jul 14 (Release) - 11 May 16 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   8.75

Chains :   Asym./Biol. Unit : P,X

Keywords :   Translation, Termination, Recycling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Preis, A. Heuer, C. Barrio-Garcia, A. Hauser, D. E. Eyler, O. Berninghausen, R. Green, T. Becker, R. Beckmann
Cryoelectron Microscopic Structures Of Eukaryotic Translation Termination Complexes Containing Erf1-Erf3 Or Erf1-Abce1.
Cell Rep. V. 8 59 2014
PubMed-ID: 25001285 | Reference-DOI: 10.1016/J.CELREP.2014.04.058

Molecule 1 - TRANSLATION INITIATION FACTOR RLI1
	Chains	:	P
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PYES2
	Expression System Taxid	:	4932
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	ATP-BINDING CASSETTE SUB-FAMILY E MEMBER RLI1, RNASE L INHIBITOR, ABCE1 IN RIBOSOME BOUND ERF1-ABCE1-ADPNP COMPLEX

Molecule 2 - EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	EUKARYOTIC RELEASE FACTOR 1, ERF1, OMNIPOTENT SUPPRESSOR PROTEIN 1, ERF1 IN RIBOSOME-BOUND ERF1-ABCE1-ADPNP COMPLEX

		1	2
Asymmetric/Biological Unit	:	P	X

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH P:1903 , TYR P:87 , PHE P:92 , ASN P:112 , GLY P:113 , ILE P:114 , GLY P:115 , LYS P:116 , SER P:117 , THR P:118 , SER P:299 , MG P:1613	BINDING SITE FOR RESIDUE ATP P1609
2	AC2	SOFTWARE	CYS P:29 , CYS P:38 , ILE P:50 , CYS P:55 , CYS P:58 , GLY P:59 , CYS P:61 , ILE P:72	BINDING SITE FOR RESIDUE SF4 P1610
3	AC3	SOFTWARE	CYS P:16 , LYS P:17 , PRO P:18 , CYS P:21 , ARG P:22 , GLU P:24 , CYS P:25 , CYS P:65 , PRO P:66 , PHE P:67 , ALA P:69	BINDING SITE FOR RESIDUE SF4 P1611
4	AC4	SOFTWARE	ARG P:217 , GLN P:363 , PHE P:366 , GLU P:386 , ASN P:387 , GLY P:388 , THR P:389 , GLY P:390 , LYS P:391 , THR P:392 , THR P:393 , SER P:546	BINDING SITE FOR RESIDUE ADP P1612
5	AC5	SOFTWARE	SER P:117 , GLN P:171 , ATP P:1609	BINDING SITE FOR RESIDUE MG P1613

(no "SS Bond" information available for 4CRM)

(no "Cis Peptide Bond" information available for 4CRM)

(no "SAP(SNP)/Variant" information available for 4CRM)

Asymmetric/Biological Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	RLI1_YEAST	7-31 46-75	2	P:7-31 P:46-75
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	RLI1_YEAST	55-66	1	P:55-66
3	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	RLI1_YEAST	468-482	1	P:468-482

(no "Exon" information available for 4CRM)

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 P from PDB  Type:PROTEIN  Length:608
 aligned with RLI1_YEAST | Q03195 from UniProtKB/Swiss-Prot  Length:608

    Alignment length:608
                                    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        
           RLI1_YEAST     1 MSDKNSRIAIVSADKCKPKKCRQECKRSCPVVKTGKLCIEVTPTSKIAFISEILCIGCGICVKKCPFDAIQIINLPTNLEAHVTHRYSANSFKLHRLPTPRPGQVLGLVGTNGIGKSTALKILAGKQKPNLGRFDDPPEWQEIIKYFRGSELQNYFTKMLEDDIKAIIKPQYVDNIPRAIKGPVQKVGELLKLRMEKSPEDVKRYIKILQLENVLKRDIEKLSGGELQRFAIGMSCVQEADVYMFDEPSSYLDVKQRLNAAQIIRSLLAPTKYVICVEHDLSVLDYLSDFVCIIYGVPSVYGVVTLPASVREGINIFLDGHIPAENLRFRTEALQFRIADATEDLQNDSASRAFSYPSLKKTQGDFVLNVEEGEFSDSEILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKIRGQFLNPQFQTDVVKPLRIDDIIDQEVQHLSGGELQRVAIVLALGIPADIYLIDEPSAYLDSEQRIICSKVIRRFILHNKKTAFIVEHDFIMATYLADKVIVFEGIPSKNAHARAPESLLTGCNRFLKNLNVTFRRDPNSFRPRINKLDSQMDKEQKSSGNYFFLDNTGI 608
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.................hhhhhhh...eeee....eeee........hhhhhhh....eeeeee.......eeee......eee.........eeeee.....hhhhhhhhhhh.............hhhhhhhhh...hhhhhhhhhhhh....eee.....hhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhh.hhhhh......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhh.eeeeee.......ee...eehhhhhhhhhhhee....ee..........................ee..eeee....eeee..ee.....eeeee.....hhhhhhhhhhh..............eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.eeee.eee...eee....eehhhhhhhhhhhhh..................hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------4FE4S_FER_2  PDB: P:7-31 --------------4FE4S_FER_2  PDB: P:46-75     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------4FE4S_FER_1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4crm P   1 MSDKNSRIAIVSADKCKPKKCRQECKRSCPVVKTGKLCIEVTPTSKIAFISEILCIGCGICVKKCPFDAIQIINLPTNLEAHVTHRYSANSFKLHRLPTPRPGQVLGLVGTNGIGKSTALKILAGKQKPNLGRFDDPPEWQEIIKYFRGSELQNYFTKMLEDDIKAIIKPQYVDNIPRAIKGPVQKVGELLKLRMEKSPEDVKRYIKILQLENVLKRDIEKLSGGELQRFAIGMSCVQEADVYMFDEPSSYLDVKQRLNAAQIIRSLLAPTKYVICVEHDLSVLDYLSDFVCIIYGVPSVYGVVTLPASVREGINIFLDGHIPAENLRFRTEALQFRIADATEDLQNDSASRAFSYPSLKKTQGDFVLNVEEGEFSDSEILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKIRGQFLNPQFQTDVVKPLRIDDIIDQEVQHLSGGELQRVAIVLALGIPADIYLIDEPSAYLDSEQRIICSKVIRRFILHNKKTAFIVEHDFIMATYLADKVIVFEGIPSKNAHARAPESLLTGCNRFLKNLNVTFRRDPNSFRPRINKLDSQMDKEQKSSGNYFFLDNTGI 608
                                    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

Chain X from PDB  Type:PROTEIN  Length:282
 aligned with ERF1_YEAST | P12385 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:282
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419  
           ERF1_YEAST   140 DDKFGFIVMDGQGTLFGSVSGNTRTVLHKFTVDLPKKHGRGGQSALRFARLREEKRHNYVRKVAEVAVQNFITNDKVNVKGLILAGSADFKTDLAKSELFDPRLACKVISIVDVSYGGENGFNQAIELSAEALANVKYVQEKKLLEAYFDEISQDTGKFCYGIDDTLKALDLGAVEKLIVFENLETIRYTFKDAEDNEVIKFAEPEAKDKSFAIDKATGQEMDVVSEEPLIEWLAANYKNFGATLEFITDKSSEGAQFVTGFGGIGAMLRYKVNFEQLVDES 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....eeeeeee..eeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhh.......hhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh..eeeee.......eeeeee....eeeeee....hhhhhh...........eeeeeehhhhhhhhhhhhh..ee.......hhhhhhhh.....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4crm X 140 DDKFGFIVMDGQGTLFGSVSGNTRTVLHKFTVDLPKKHGRGGQSALRFARLREEKRHNYVRKVAEVAVQNFITNDKVNVKGLILAGSADFKTDLAKSELFDPRLACKVISIVDVSYGGENGFNQAIELSAEALANVKYVQEKKLLEAYFDEISQDTGKFCYGIDDTLKALDLGAVEKLIVFENLETIRYTFKDAEDNEVIKFAEPEAKDKSFAIDKATGQEMDVVSEEPLIEWLAANYKNFGATLEFITDKSSEGAQFVTGFGGIGAMLRYKVNFEQLVDES 421
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419

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 4CRM)

(no "CATH Domain" information available for 4CRM)

(no "Pfam Domain" information available for 4CRM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (RLI1_YEAST | Q03195)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0042273	ribosomal large subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0000054	ribosomal subunit export from nucleus	The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
	GO:0032790	ribosome disassembly	The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits.
	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.
	GO:0006415	translational termination	The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0022626	cytosolic ribosome	A ribosome located in the cytosol.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain X (ERF1_YEAST | P12385)

molecular function
	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:0003747	translation release factor activity	Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
	GO:0016149	translation release factor activity, codon specific	A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
biological process
	GO:0006353	DNA-templated transcription, termination	The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
	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:0006415	translational termination	The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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:0018444	translation release factor complex	A heterodimeric complex involved in the release of a nascent polypeptide chain from a ribosome.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4crm)

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	4crm
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	RLI1_YEAST \| Q03195
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UniProtKB/Swiss-Prot
	ERF1_YEAST \| P12385	:	4crn
	RLI1_YEAST \| Q03195	:	3j16 5ll6

4crn	CRYO-EM OF A PRETERMINATION COMPLEX WITH ERF1 AND ERF3 RELATED ID: EMD-2598 RELATED DB: EMDB

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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