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Title :   CRYSTAL STRUCTURE OF NRO1/ETT1 PROTEIN FROM S. POMBE (HIGH RESOLUTION)

Authors :   D. Rispal, J. Henri, H. Van Tilbeurgh, M. Graille, B. Seraphin

Date :   23 Feb 11 (Deposition) - 21 Sep 11 (Release) - 14 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Tetratricopeptide Repeat, Enhancer Of Translation Termination, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Rispal, J. Henri, H. Van Tilbeurgh, M. Graille, B. Seraphin
Structural And Functional Analysis Of Nro1/Ett1: A Protein Involved In Translation Termination In S. Cerevisiae And In O2-Mediated Gene Control In S. Pombe
Rna V. 17 1213 2011
PubMed-ID: 21610214 | Reference-DOI: 10.1261/RNA.2697111

Molecule 1 - UNCHARACTERIZED PROTEIN C4B3.07
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21-A
	Expression System Strain	:	ROSETTA PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 56-393
	Gene	:	SPCC4B3.07
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

		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 (5, 15)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:101 , ARG A:104 , ASN A:105	BINDING SITE FOR RESIDUE SO4 A 2
2	AC2	SOFTWARE	ALA A:276 , HOH A:470	BINDING SITE FOR RESIDUE CL A 1
3	AC3	SOFTWARE	TRP A:70 , HOH A:597 , HOH A:627	BINDING SITE FOR RESIDUE EDO A 394
4	AC4	SOFTWARE	ARG B:101 , ARG B:104 , ASN B:105	BINDING SITE FOR RESIDUE SO4 B 1
5	AC5	SOFTWARE	ARG B:167 , PHE B:224 , ASP B:225 , HOH B:400 , HOH B:445	BINDING SITE FOR RESIDUE EDO B 394
6	AC6	SOFTWARE	PHE A:93 , HIS A:97 , GLU B:191	BINDING SITE FOR RESIDUE EDO B 395

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

(no "Cis Peptide Bond" information available for 3QTM)

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

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

(no "Exon" information available for 3QTM)

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:329
 aligned with ETT1_SCHPO | Q9USJ7 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:333
                                    68        78        88        98       108       118       128       138       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   
           ETT1_SCHPO    59 VYTEEDNISQLWGLYEMSREKLENDDIDASVSLVFGTIHEADRILRNTEDISTLPKDFHAAYSSALLAVSELFEIAQKRLKETNTEESYIDAAIERAQLGLDAPGNESRLFLALARAYLEKVRVLVWRHDNEESLANIPVTQLVNPYIEKAIQYLRPLAQDSTEYFDALTPDSLRPLYILSSYLFQFGDQFSEAFLLDVCSIITALWLKSVVDPNTPAYYKLIAQEAVLNNYTTFAEYYMDLLDNSESNVDDLINKASSWLNNSVDTWNVIYTLDKSPERLLKLADIKMDLAQIVQDEASQDNYLKEACNAIKEAQGSGVELSPDYVEFVEAY 391
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.----hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qtm A  59 VYTEEDNISQLWGLYEmSREKLENDDIDASVSLVFGTIHEADRILRNTEDISTLPKDFHAAYSSALLAVSELFEIAQKRLKETNTEESYIDAAIERAQLGLDAPGNESRLFLALARAYLEKVRVLVWRHDNEESLANIPVTQLVNPYIEKAIQYLRPLAQDSTEYFDALTPDSLRPLYILSSYLFQFGDQFSEAFLLDVcSIITALWLKSVVDPNTPAYYKLIAQEAVLNNYTTFAEYYmDLLDN----VDDLINKASSWLNNSVDTWNVIYTLDKSPERLLKLADIKmDLAQIVQDEASQDNYLKEACNAIKEAQGSGVELSPDYVEFVEAY 391
                                    68      | 78        88        98       108       118       128       138       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   
                                           75-MSE                                                                                                                                                                                258-CME                                 298-MSE3  308                                    347-MSE

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with ETT1_SCHPO | Q9USJ7 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:332
                                    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  
           ETT1_SCHPO    61 TEEDNISQLWGLYEMSREKLENDDIDASVSLVFGTIHEADRILRNTEDISTLPKDFHAAYSSALLAVSELFEIAQKRLKETNTEESYIDAAIERAQLGLDAPGNESRLFLALARAYLEKVRVLVWRHDNEESLANIPVTQLVNPYIEKAIQYLRPLAQDSTEYFDALTPDSLRPLYILSSYLFQFGDQFSEAFLLDVCSIITALWLKSVVDPNTPAYYKLIAQEAVLNNYTTFAEYYMDLLDNSESNVDDLINKASSWLNNSVDTWNVIYTLDKSPERLLKLADIKMDLAQIVQDEASQDNYLKEACNAIKEAQGSGVELSPDYVEFVEAYS 392
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qtm B  61 TEEDNISQLWGLYEmSREKLENDDIDASVSLVFGTIHEADRILRNTEDISTLPKDFHAAYSSALLAVSELFEIAQKRLKETNTEESYIDAAIERAQLGLDAPGNESRLFLALARAYLEKVRVLVWRHDNEESLANIPVTQLVNPYIEKAIQYLRPLAQDSTEYFDALTPDSLRPLYILSSYLFQFGDQFSEAFLLDVcSIITALWLKSVVDPNTPAYYKLIAQEAVLNNYTTFAEYYmDLLDN----VDDLINKASSWLNNSVDTWNVIYTLDKSPERLLKLADIKmDLAQIVQDEASQDNYLKEACNAIKEAQGSGVELSPDYVEFVEAYS 392
                                    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  
                                         75-MSE                                                                                                                                                                                258-CME                                 298-MSE3  308                                    347-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 3QTM)

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

(no "Pfam Domain" information available for 3QTM)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ETT1_SCHPO | Q9USJ7)

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).
biological process
	GO:0032933	SREBP signaling pathway	A series of molecular signals from the endoplasmic reticulum to the nucleus generated as a consequence of decreased levels of one or more sterols (and in some yeast, changes in oxygen levels) and which proceeds through activation of a sterol response element binding transcription factor (SREBP) to result in up-regulation of target gene transcription.
	GO:2000640	positive regulation of SREBP signaling pathway	Any process that activates or increases the frequency, rate or extent of the SREBP signaling pathway.
	GO:1900039	positive regulation of cellular response to hypoxia	Any process that activates or increases the frequency, rate or extent of cellular response to hypoxia.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0061419	positive regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	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: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.

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	ETT1_SCHPO \| Q9USJ7	:	3msv 3qtn

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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