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Title :   CRYO-EM OF A PRETERMINATION COMPLEX WITH ERF1 AND ERF3

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 :   9.10

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

Keywords :   Translation, Termination, Cryo-Em (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 - ERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX
	Chains	:	P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB2
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	FOR CHAIN P (ERF3) THE FIRST 254 AMINO ACIDS ARE MISSING.

Molecule 2 - ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB2
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	FOR CHAIN X THE LAST 25 AMINO ACIDS (416-440) ARE MISSING

		1	2
Asymmetric/Biological Unit	:	P	X

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS P:267 , VAL P:268 , ASP P:269 , ALA P:270 , GLY P:271 , LYS P:272 , SER P:273 , GLN P:304 , GLY P:305 , TYR P:307 , LYS P:323 , THR P:324 , ILE P:325 , ASP P:343 , ALA P:344 , PRO P:345 , GLY P:346 , LYS P:348 , ASN P:405 , LYS P:406 , ASP P:409 , GLY P:448	BINDING SITE FOR RESIDUE GNP P1685

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

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

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

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.	ERF3_YEAST	314-329	1	P:313-328

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR172W	1	YDR172W.1	IV:808322-810379	2058	ERF3_YEAST	1-685	685	1	P:255-684	430

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:430
 aligned with ERF3_YEAST | P05453 from UniProtKB/Swiss-Prot  Length:685

    Alignment length:430
                                   265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685
           ERF3_YEAST   256 GGKDHVSLIFMGHVDAGKSTMGGNLLYLTGSVDKRTIEKYEREAKDAGRQGWYLSWVMDTNKEERNDGKTIEVGKAYFETEKRRYTILDAPGHKMYVSEMIGGASQADVGVLVISARKGEYETGFERGGQTREHALLAKTQGVNKMVVVVNKMDDPTVNWSKERYDQCVSNVSNFLRAIGYNIKTDVVFMPVSGYSGANLKDHVDPKECPWYTGPTLLEYLDTMNHVDRHINAPFMLPIAAKMKDLGTIVEGKIESGHIKKGQSTLLMPNKTAVEIQNIYNETENEVDMAMCGEQVKLRIKGVEEEDISPGFVLTSPKNPIKSVTKFVAQIAIVELKSIIAAGFSCVMHVHTAIEEVHIVKLLHKLEKGTNRKSKKPPAFAKKGMKVIAVLETEAPVCVETYQDYPQLGRFTLRDQGTTIAIGKIVKIAE 685
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee....hhhhhhhhhhh........hhhhhh................hhhhhhh..............................hhhhhhhh........eeee..hhhhhhhh.......hhhhhh..........eee.............hhhhhhhhhhhhhh............ee..........................hhhhhh............eeeeeeeee...eeeeee..........eeee....eeeeeeeee..............eeeeee............eee...........eeeeeee...........eeeee....eeeee..............................eeeee................eeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------G_TR_1          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: P:255-684 UniProt: 1-685 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                 4crn P 255 GGKDHVSLIFMGHVDAGKSTMGGNLLYLTGSVDKRTIEKYEREAKDAGRQGWYLSWVMDTNKEERNDGKTIEVGKAYFETEKRRYTILDAPGHKMYVSEMIGGASQADVGVLVISARKGEYETGFERGGQTREHALLAKTQGVNKMVVVVNKMDDPTVNWSKERYDQCVSNVSNFLRAIGYNIKTDVVFMPVSGYSGANLKDHVDPKECPWYTGPTLLEYLDTMNHVDRHINAPFMLPIAAKMKDLGTIVEGKIESGHIKKGQSTLLMPNKTAVEIQNIYNETENEVDMAMCGEQVKLRIKGVEEEDISPGFVLTSPKNPIKSVTKFVAQIAIVELKSIIAAGFSCVMHVHTAIEEVHIVKLLHKLEKGTNRKSKKPPAFAKKGMKVIAVLETEAPVCVETYQDYPQLGRFTLRDQGTTIAIGKIVKIAE 684
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684

Chain X from PDB  Type:PROTEIN  Length:422
 aligned with ERF1_YEAST | P12385 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:422
                                    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  
           ERF1_YEAST     1 MDNEVEKNIEIWKVKKLVQSLEKARGNGTSMISLVIPPKGQIPLYQKMLTDEYGTASNIKSRVNRLSVLSAITSTQQKLKLYNTLPKNGLVLYCGDIITEDGKEKKVTFDIEPYKPINTSLYLCDNKFHTEVLSELLQADDKFGFIVMDGQGTLFGSVSGNTRTVLHKFTVDLPKKHGRGGQSALRFARLREEKRHNYVRKVAEVAVQNFITNDKVNVKGLILAGSADFKTDLAKSELFDPRLACKVISIVDVSYGGENGFNQAIELSAEALANVKYVQEKKLLEAYFDEISQDTGKFCYGIDDTLKALDLGAVEKLIVFENLETIRYTFKDAEDNEVIKFAEPEAKDKSFAIDKATGQEMDVVSEEPLIEWLAANYKNFGATLEFITDKSSEGAQFVTGFGGIGAMLRYKVNFEQLVDESE 422
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........eeeeee...........eeeee.........eee........hhhhhh.....eeeee......eeeeee..eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.....eeee....hhhhhh.......hhhhh..eee....hhhhhhhhhhhhh..........hhhhhhhhhhhhh............hhhhhhh....eeeee.......ee........ee........hhhhhh...............................eee...hhhhhhhhhhh..eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4crn X   1 MDNEVEKNIEIWKVKKLVQSLEKARGNGTSMISLVIPPKGLIPLYQKMLTDEYGTASNIKSRVNRLSVLSAITSTQQKLKLYNTLPKNGLVLYCGDIITEDGKEKKVTFDIEPYKPINTSLYLCDNKFHTEVLSELLQADDKFGFIVMDGQGTLFGSVSGNTRTVLHKFTVDLPKKHGRGGQSALRFARLREEKRHNYVRKVAEVAVQNFITNDKVNVKGLILAGSADFKTDLAKSELFDPRLACKVISIVDVSYGGENGFNQAIELSAEALANVKYVQEKKLLEAYFDEISQDTGKFCFGIDDTLKALDLGAVEKLIVFENLETIRYTFKDAEDNEVIKFAEPEAKDKSFAIDKATGQEMDVVSEEPLIEWLAANYKNFGATLEFITDKSSEGAQFVTGFGGIGAMLRYKVNFEQLVDESE 422
                                    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

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 4CRN)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (ERF3_YEAST | P05453)

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: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.
biological process
	GO:0002184	cytoplasmic translational termination	The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon.
	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
	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.

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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	4crn
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	ERF3_YEAST \| P05453
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	ERF1_YEAST \| P12385
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UniProtKB/Swiss-Prot
	ERF1_YEAST \| P12385	:	4crm
	ERF3_YEAST \| P05453	:	1yjo 1yjp 2omm 5k2e 5k2f 5k2g 5k2h

4crm	CRYO-EM OF A PRE-RECYCLING COMPLEX WITH ERF1 AND ABCE1 RELATED ID: EMD-2597 RELATED DB: EMDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (15, 23)

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