3P27 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF S. CEREVISIAE HBS1 PROTEIN (GDP-BOUND FORM), A TRANSLATIONAL GTPASE INVOLVED IN RNA QUALITY CONTROL PATHWAYS AND INTERACTING WITH DOM34/PELOTA

Authors :   A. Van Den Elzen, J. Henri, N. Lazar, M. E. Gas, D. Durand, F. Lacroute, M. Nicaise, H. Van Tilbeurgh, B. Sraphin, M. Graille, Paris-Sud Yea Structural Genomics (Ysg)

Date :   01 Oct 10 (Deposition) - 17 Nov 10 (Release) - 14 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Gdp/Gtp Binding Domain, Beta-Barrel, Translational Gtpase, Structural Genomics, Paris-Sud Yeast Structural Genomics, Ysg, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Van Den Elzen, J. Henri, N. Lazar, M. E. Gas, D. Durand, F. Lacroute, M. Nicaise, H. Van Tilbeurgh, B. Seraphin, M. Graille
Dissection Of Dom34-Hbs1 Reveals Independent Functions In Two Rna Quality Control Pathways.
Nat. Struct. Mol. Biol. V. 17 1446 2010
PubMed-ID: 21102444 | Reference-DOI: 10.1038/NSMB.1963

Molecule 1 - ELONGATION FACTOR 1 ALPHA-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HBS1, YKR084C, YKR404
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 20)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:175 , VAL A:176 , ASP A:177 , ALA A:178 , GLY A:179 , LYS A:180 , SER A:181 , THR A:182 , ASN A:313 , LYS A:314 , ASP A:316 , ASN A:317 , SER A:352 , GLY A:353 , PHE A:354	BINDING SITE FOR RESIDUE GDP A 663
2	AC2	SOFTWARE	HIS B:175 , VAL B:176 , ASP B:177 , ALA B:178 , GLY B:179 , LYS B:180 , SER B:181 , THR B:182 , ASN B:313 , LYS B:314 , ASP B:316 , ASN B:317 , SER B:352 , GLY B:353 , PHE B:354	BINDING SITE FOR RESIDUE GDP B 663

(no "SS Bond" information available for 3P27)

Asymmetric Unit

No.	Residues
1	Tyr A:439	-	Pro A:440
2	Tyr B:439	-	Pro B:440

(no "SAP(SNP)/Variant" information available for 3P27)

Asymmetric Unit (1, 2)

	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.	HBS1_YEAST	221-236	2	A:221-236 B:221-236

Biological Unit 1 (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.	HBS1_YEAST	221-236	1	A:221-236 -

Biological Unit 2 (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.	HBS1_YEAST	221-236	1	- B:221-236

(no "Exon" information available for 3P27)

Asymmetric 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:433
 aligned with HBS1_YEAST | P32769 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:473
                                   148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608   
           HBS1_YEAST   139 VQRYYKTTVPTKPKKPHDISAFVKSALPHLSFVVLGHVDAGKSTLMGRLLYDLNIVNQSQLRKLQRESETMGKSSFKFAWIMDQTNEERERGVTVSICTSHFSTHRANFTIVDAPGHRDFVPNAIMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWYNGPNLMSTLENAAFKISKENEGINKDDPFLFSVLEIIPSKKTSNDLALVSGKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQGQSTNHEETDVAIKGDFVTLKLRKAYPEDIQNGDLAASVDYSSIHSAQCFVLELTTFDMNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNTASKKKIRHLGSKQRAFVEIELIEVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ 611
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhh..eeeeeeee....hhhhhhhhhhhhh.....hhhhhhh.-------------hhhhhh-------.....eeeeee....eeeeee...----hhhhhhhhhhh.eeeeeee...------...hhhhhhhhhhhhhh....eeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhh.hhh.eeeee..............hhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeeeee...-----.eeeeeeeee.ee....eeeee...eeeeeeeee.....-----..ee..ee...eeeeeee..hhhhh....eee.......ee..eeeeeeee...........eeeeee..eeeeeeeeeeeee...................eeeeeeee.......ee..........eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p27 A 139 VQRYYKTTVPTKPKKPHDISAFVKSALPHLSFVVLGHVDAGKSTLmGRLLYDLNIVNQSQLRKLQR-------------WImDQT-------VTVSICTSHFSTHRANFTIVDAPG----VPNAImGISQADmAILCVDCST------FDLDGQTKEHmLLASSLGIHNLIIAmNKmDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWYNGPNLmSTLENAAFKISKENEGINKDDPFLFSVLEIIPSK-----LALVSGKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQ-----HEETDVAIKGDFVTLKLRKAYPEDIQNGDLAASVDYSSIHSAQCFVLELTTFDmNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNTASKKKIRHLGSKQRAFVEIELIEVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ 611
                                   148       158       168       178     | 188       198     |   -       218 |  |    -  |    238       248     |   -|    | 268  |    278 |     288       298       308   |  |318       328       338       348       358       368       378       388       398       408   |   418       428       438       448       | -   |   468       478       488       498       508      |518       528       538       548       558       568       578       588       598       608   
                                                                       184-MSE             204           218 |  |     231                    254  259    |      |      280    287       297-MSE        312-MSE                                                           378-MSE                           412   418                                   456   462                                                  515-MSE                                                                                            
                                                                                                           220-MSE                                     264-MSE  |                                         315-MSE                                                                                                                                                                                                                                                                                                    
                                                                                                              223                                             271-MSE

Chain B from PDB  Type:PROTEIN  Length:444
 aligned with HBS1_YEAST | P32769 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:473
                                   148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608   
           HBS1_YEAST   139 VQRYYKTTVPTKPKKPHDISAFVKSALPHLSFVVLGHVDAGKSTLMGRLLYDLNIVNQSQLRKLQRESETMGKSSFKFAWIMDQTNEERERGVTVSICTSHFSTHRANFTIVDAPGHRDFVPNAIMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWYNGPNLMSTLENAAFKISKENEGINKDDPFLFSVLEIIPSKKTSNDLALVSGKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQGQSTNHEETDVAIKGDFVTLKLRKAYPEDIQNGDLAASVDYSSIHSAQCFVLELTTFDMNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNTASKKKIRHLGSKQRAFVEIELIEVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ 611
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------GTP_EFTU-3p27B01 B:165-410                                                                                                                                                                                                                                   -GTP_EFTU_D2-3p27B03 B:419-493                                              ---------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------GTP_EFTU-3p27B02 B:165-410                                                                                                                                                                                                                                   -GTP_EFTU_D2-3p27B04 B:419-493                                              ---------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .................hhhhhhhhh..eeeeeeee....hhhhhhhhhhhhh...hhhhhhhhh.------------hhhhhhh............eeeeee....eeeeee......hhhhhhhhhhhh.eeeeeee...------...hhhhhhhhhhhhhh....eeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhh.hhh.eeeee..............hhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeeeee.-------.eeeeeeeee.ee....eeeee...eeeeeeeee......----..ee..ee...eeeeeee..hhhhh....eee.......ee..eeeeeeee...........eeeeee..eeeeeeeeeeeee...................eeeeeeee.......ee..........eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p27 B 139 VQRYYKTTVPTKPKKPHDISAFVKSALPHLSFVVLGHVDAGKSTLmGRLLYDLNIVNQSQLRKLQR------------AWImDQTNEERERGVTVSICTSHFSTHRANFTIVDAPGHRDFVPNAImGISQADmAILCVDCST------FDLDGQTKEHmLLASSLGIHNLIIAmNKmDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWYNGPNLmSTLENAAFKISKENEGINKDDPFLFSVLEIIP-------LALVSGKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQG----HEETDVAIKGDFVTLKLRKAYPEDIQNGDLAASVDYSSIHSAQCFVLELTTFDmNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNTASKKKIRHLGSKQRAFVEIELIEVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ 611
                                   148       158       168       178     | 188       198     |   -       218 |     228       238       248       258     | 268  |    278 |     288       298       308   |  |318       328       338       348       358       368       378       388       398       408 |     418       428       438       448        |-   |   468       478       488       498       508      |518       528       538       548       558       568       578       588       598       608   
                                                                       184-MSE             204          217  |                                         264-MSE  |      280    287       297-MSE        312-MSE                                                           378-MSE                         410     418                                    457  462                                                  515-MSE                                                                                            
                                                                                                           220-MSE                                            271-MSE                                     315-MSE

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 3P27)

(no "CATH Domain" information available for 3P27)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HBS1_YEAST | P32769)

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:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0070651	nonfunctional rRNA decay	An rRNA catabolic process that results in the targeted detection and degradation of aberrant rRNAs contained within translationally defective ribosomes, thereby acting as a quality-control system.
	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: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: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:1990533	Dom34-Hbs1 complex	A protein complex consisting of one subunit known as Dom34 or Pelota that has similarity to translation termination factor eRF1, and another subunit, Hbs1, that is a GTPase with similarity to translation termination factor eRF3. The Dom34-Hbs1 complex has a role in cotranslational mRNA quality control by promoting ribosomal subunit dissociation and peptidyl-tRNA release when translation is stalled, facilitating no-go decay and nonstop decay.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Tyr A:439 - Pro A:440	[ RasMol ]
		Tyr B:439 - Pro B:440	[ RasMol ]

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	3p27
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	HBS1_YEAST \| P32769
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	HBS1_YEAST \| P32769	:	3izq 3p26 5m1j

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 20)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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