3MCA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE DOM34-HBS1 COMPLEX AND IMPLICATIONS FOR ITS ROLE IN NO-GO DECAY

Authors :   L. Chen, H. Song

Date :   28 Mar 10 (Deposition) - 06 Oct 10 (Release) - 20 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.74

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein Protein Complex, Translation Regulation, No-Go Decay, Translation Regulation-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Chen, D. Muhlrad, V. Hauryliuk, Z. Cheng, M. K. Lim, V. Shyp, R. Parker, H. Song
Structure Of The Dom34-Hbs1 Complex And Implications For No-Go Decay
Nat. Struct. Mol. Biol. V. 17 1233 2010
PubMed-ID: 20890290 | Reference-DOI: 10.1038/NSMB.1922

Molecule 1 - ELONGATION FACTOR 1 ALPHA-LIKE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Synonym	:	HBS1

Molecule 2 - PROTEIN DOM34
	Chains	:	B
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3MCA)

(no "Site" information available for 3MCA)

(no "SS Bond" information available for 3MCA)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:159	-	Thr A:160
2	Leu A:298	-	Glu A:299
3	Lys B:77	-	Ala B:78
4	Ala B:128	-	Cys B:129
5	Cys B:129	-	Asn B:130

(no "SAP(SNP)/Variant" information available for 3MCA)

(no "PROSITE Motif" information available for 3MCA)

(no "Exon" information available for 3MCA)

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:377
 aligned with HBS1_SCHPO | O74774 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:438
                                   164       174       184       194       204       214       224       234       244       254       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        
           HBS1_SCHPO   155 KKQNPTDLVSVPEIFEQSNPKPVVHLVVTGHVDSGKSTMLGRIMFELGEINSRSMQKLHNEAANSGKGSFSYAWLLDTTEEERARGVTMDVASTTFESDKKIYEIGDAPGHRDFISGMIAGASSADFAVLVVDSSQNNFERGFLENGQTREHAYLLRALGISEIVVSVNKLDLMSWSEDRFQEIKNIVSDFLIKMVGFKTSNVHFVPISAISGTNLIQKDSSDLYKWYKGPTLLSALDQLVPPEKPYRKPLRLSIDDVYRSPRSVTVTGRVEAGNVQVNQVLYDVSSQEDAYVKNVIRNSDPSSTWAVAGDTVTLQLADIEVNQLRPGDILSNYENPVRRVRSFVAEIQTFDIHGPILSGSTLVLHLGRTVTSVSLKIVTVNNKRSRHIASRKRALVRISFLDGLFPLCLAEECPALGRFILRRSGDTVAAGIVKELC 592
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------GTP_EFTU-3mcaA01 A:175-397                                                                                                                                                                                                     --------------------GTP_EFTU_D2-3mcaA02 A:418-486                                        ----GTP_EFTU_D3-3mcaA03 A:491-592                                                                          Pfam domains
         Sec.struct. author ............hhhhhh....eeeeeee.....hhhhhhhhhhhhhhh.------------------------------------------------------..eee...eeeee...-------...eeeeee...........hhhhhhhhhhhh....eeeeee.hhhhh.hhhhhhhhhhhhhhhhh.....hhh.eeeeee.............hhhhhh....hhhhhhhh............eeeeeeeeee..eeeeeeeeee.eee...eeee....eeeeeeeee........eee...eeeeee...hhhhh....eee......eee.eeeeeeee......ee..eeeeee....eeeeeeeeee.......ee....eeeeeeee....eee.....hhhhheeeee....eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mca A 155 KKQNPTDLVSVPEIFEQSNPKPVVHLVVTGHVDSGKSTMLGRIMFELGEI------------------------------------------------------IGDAPGHRDFISGMIA-------AVLVVDSSQNNFERGFLENGQTREHAYLLRALGISEIVVSVNKLDLMSWSEDRFQEIKNIVSDFLIKMVGFKTSNVHFVPISAISGTNLIQKDSSDLYKWYKGPTLLSALDQLVPPEKPYRKPLRLSIDDVYRSPRSVTVTGRVEAGNVQVNQVLYDVSSQEDAYVKNVIRNSDPSSTWAVAGDTVTLQLADIEVNQLRPGDILSNYENPVRRVRSFVAEIQTFDIHGPILSGSTLVLHLGRTVTSVSLKIVTVNNKRSRHIASRKRALVRISFLDGLFPLCLAEECPALGRFILRRSGDTVAAGIVKELC 592
                                   164       174       184       194       204         -         -         -         -         -    |  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        
                                                                           204                                                    259            274     282

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with DOM34_SCHPO | Q9USL5 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:372
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377  
          DOM34_SCHPO     8 IEKNGSGWITMCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSRVVMKLRILVENMDFDTKAAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAFALDRVDAACNPSRNAEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQSINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSLFRSSDIATRKKWVSLVEGVKEINCPVYIFSSLHESGKQLDLLSGIAAILTYPVDEEDISEDE 379
               SCOP domains ---- ------   ------------------------                    ------------------- -------   ------------------ ----------------d3  mcab1 B:131-271 automated matches                                                                                                        d3mcab2 B:272-379 automated matches                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains eRF1 _1-3mc   aB03 B:8-131                                                                                                  -  -eRF1_2-3mcaB02 B:136-268                                                                                                             --eRF1_3-3mcaB01 B:271-370                                                                            --------- Pfam domains
         Sec.struct. author ....-....ee---.hhhhhhhhhhh....ee......--------------------.ee...eee......eee.-.......---..............ee..-...hhhhhhhhh......--..eeeeeee..eeeeeee....eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhh..eeeee....hhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh......eeee......hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhh..eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mca B   8 IEKN-SGWITM---EPEDMWHLYNILQVGDQLKASTVR--------------------RILVENMDFDTKAAQLHIK-RTTEYHP---MGSYHTLDLELHRNFTLY-NEWDAFALDRVDAACNPS--AEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQSINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIHSLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSLFRSSDIATRKKWVSLVEGVKEINCPVYIFSSLHESGKQLDLLSGIAAILTYPVDEEDISEDE 379
                               | |  17|   |   27        37       | -         -        67        77      | 87    |   97       107     | 117       127    |  137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377  
                              11 |   18  22                     45                   66                84 |    92  96              113 |              132  |                                                                                                                                                                                                                                                    
                                13                                                                       86                          115                 135

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 3MCA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HBS1_SCHPO | O74774)

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:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0002181	cytoplasmic translation	The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
	GO:0002182	cytoplasmic translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm.
	GO:0006417	regulation of translation	Any process that modulates 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: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: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.

Chain B (DOM34_SCHPO | Q9USL5)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0071025	RNA surveillance	The set of processes involved in identifying and degrading defective or aberrant RNAs.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051321	meiotic cell cycle	Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
	GO:0070317	negative regulation of G0 to G1 transition	A cell cycle process that stops, prevents, or reduces the rate or extent of the transition from the G0 quiescent state to the G1 phase.
	GO:0000294	nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay	A minor degradation pathway nuclear-transcribed mRNAs that begins with an endonucleolytic cleavage to generate unprotected ends.
	GO:0070966	nuclear-transcribed mRNA catabolic process, no-go decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
	GO:0070481	nuclear-transcribed mRNA catabolic process, non-stop decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0032790	ribosome disassembly	The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits.
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: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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3mca)

	Sites
(no "Sites" information available for 3mca)

	Cis Peptide Bonds
		Ala B:128 - Cys B:129	[ RasMol ]
		Cys B:129 - Asn B:130	[ RasMol ]
		Leu A:298 - Glu A:299	[ RasMol ]
		Lys B:77 - Ala B:78	[ RasMol ]
		Pro A:159 - Thr A:160	[ RasMol ]

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	3mca
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	DOM34_SCHPO \| Q9USL5
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	HBS1_SCHPO \| O74774
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	3.1.-.-
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	DOM34_SCHPO \| Q9USL5
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	HBS1_SCHPO \| O74774
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3MCA)

(no "Related Entries Specified in the PDB File" available for 3MCA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 2)

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Pfam Domains (6, 6)

Gene Ontology (27, 30)

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