1YTU | PR0146 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR 5'-END-SPECIFIC RECOGNITION OF THE GUIDE RNA STRAND BY THE A. FULGIDUS PIWI PROTEIN

Authors :   J. B. Ma, Y. R. Yuan, G. Meister, Y. Pei, T. Tuschl, D. J. Patel

Date :   11 Feb 05 (Deposition) - 05 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D  (1x)
Biol. Unit 2: B,E,F  (1x)

Keywords :   Protein-Rna Complex, Rna Duplex, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Ma, Y. R. Yuan, G. Meister, Y. Pei, T. Tuschl, D. J. Patel
Structural Basis For 5'-End-Specific Recognition Of Guide Rna By The A. Fulgidus Piwi Protein.
Nature V. 434 666 2005
PubMed-ID: 15800629 | Reference-DOI: 10.1038/NATURE03514

*Molecule 1 - 5'-R(PAPGPAPCPAPG)-3'*
	Chains	:	C, E
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-R(PUPGPUPC)-3'*
	Chains	:	D, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - HYPOTHETICAL PROTEIN AF1318
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	224325
	Strain	:	DSM 4304
	Synonym	:	PIWI

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A		C	D
Biological Unit 2 (1x)	:		B			E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 22)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 9)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 11)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:159 , LEU A:427 , A C:1 , A C:3 , HOH C:57	BINDING SITE FOR RESIDUE MG A 428
2	AC2	SOFTWARE	GLN B:159 , LEU B:427 , A E:1 , A E:3 , HOH E:17	BINDING SITE FOR RESIDUE MG B 428

(no "SS Bond" information available for 1YTU)

(no "Cis Peptide Bond" information available for 1YTU)

(no "SAP(SNP)/Variant" information available for 1YTU)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PIWI	PS50822	Piwi domain profile.	PIWI_ARCFU	110-406	2	A:110-406 B:110-406

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PIWI	PS50822	Piwi domain profile.	PIWI_ARCFU	110-406	1	A:110-406 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PIWI	PS50822	Piwi domain profile.	PIWI_ARCFU	110-406	1	- B:110-406

(no "Exon" information available for 1YTU)

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:410
 aligned with PIWI_ARCFU | O28951 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:426
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421      
           PIWI_ARCFU     2 MEYKIVENGLTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
               SCOP domains -------------------------------------------------------------------------------------------d1ytua1 A:93-408 Hypothetical protein AF1318                                                                                                                                                                                                                                                                                ------------------- SCOP domains
               CATH domains -1ytuA01  1ytuA02 A:12-172  [code=3.40.50.2300, no name defined]                                                                                                           1ytuA01 A:3-11,A:173-427  [code=3.30.420.10, no name defined]                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....eee.hhh.eee..hhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhhhhhhh.....ee.........eeeeeeeee....eeeeeeeeee....eeeeee...ee..hhhhhhhhhhhhhhhhhhh........eeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee...eeee..------....eeeeee..eeee......----------....eeeeeeee..hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.........hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------PIWI  PDB: A:110-406 UniProt: 110-406                                                                                                                                                                                                                                                                    --------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ytu A   2 mEYKIVENGLTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGImLVLPEYNTPLYYKLKSYLINSIPSQFmRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAmVFKKDGTmLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKmKDGETKILKETVEELKKQEmVSRDVKYAILHLNETHPFWVmGD------PYEGTKVKLSSKRYLLTLLQPY----------PIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKmNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
                            |       11        21        31        41        51        61        71        81        91       101       111|      121       131       141       151       161       171       181       191       201      |211       221       231       241       251       261       271       281       291       301 |     311       321       331         -|      351       361       371     | 381       391       401       411       421      
                            |                                                                                                           112-MSE                    139-MSE                                                      200-MSE 208-MSE                                             260-MSE             280-MSE              301-MSE  310                  331        342                                377-MSE                                              
                            2-MSE                                                                                                                                                                                                                                                                                                      303

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with PIWI_ARCFU | O28951 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:427
                                    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       
           PIWI_ARCFU     1 MMEYKIVENGLTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
               SCOP domains --------------------------------------------------------------------------------------------d1ytub1 B:93-408 Hypothetical protein AF1318                                                                                                                                                                                                                                                                                ------------------- SCOP domains
               CATH domains --1ytuB01  1ytuB02 B:12-172  [code=3.40.50.2300, no name defined]                                                                                                           1ytuB01 B:3-11,B:173-427  [code=3.30.420.10, no name defined]                                                                                                                                                                                                   CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------Piwi-1ytuB01 B:110-406                                                                                                                                                                                                                                                                                   --------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------Piwi-1ytuB02 B:110-406                                                                                                                                                                                                                                                                                   --------------------- Pfam domains (2)
         Sec.struct. author ..eeee.....eee.hhh.eee..hhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhhhhh.....ee.........eeeeeeeeeee..eeeeeeeee.....eeeeee...ee..hhhhhhhhhhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee....eeee...........eeee....eeee.....eeee..eeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh....hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------PIWI  PDB: B:110-406 UniProt: 110-406                                                                                                                                                                                                                                                                    --------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ytu B   1 mmEYKIVENGLTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGImLVLPEYNTPLYYKLKSYLINSIPSQFmRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAmVFKKDGTmLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKmKDGETKILKETVEELKKQEmVSRDVKYAILHLNETHPFWVmGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEmVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKmNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
                            ||      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       
                            1-MSE                                                                                                        112-MSE                    139-MSE                                                      200-MSE 208-MSE                                             260-MSE             280-MSE              301-MSE                               339-MSE                               377-MSE                                              
                             2-MSE

Chain C from PDB  Type:RNA  Length:5
                                     
                 1ytu C   1 AGACA   5

Chain D from PDB  Type:RNA  Length:4
                                    
                 1ytu D  15 UGUC  18

Chain E from PDB  Type:RNA  Length:6
                                      
                 1ytu E   1 AGACAG   6

Chain F from PDB  Type:RNA  Length:4
                                    
                 1ytu F  15 UGUC  18

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: PIWI domain (10)

Protein domain: Hypothetical protein AF1318 (3)

Archaeoglobus fulgidus [TaxId: 2234] (3)

1a	d1ytua1	A:93-408
1b	d1ytub1	B:93-408

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.10, no name defined] (372)

[unclassified] (102)

1a	1ytuA01	A:3-11,A:173-427
1b	1ytuB01	B:3-11,B:173-427

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

[unclassified] (27)

2a	1ytuA02	A:12-172
2b	1ytuB02	B:12-172

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: Piwi (16)

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (3)

1a	Piwi-1ytuB01	B:110-406
1b	Piwi-1ytuB02	B:110-406

Asymmetric Unit(hide GO term definitions)

Chain A,B (PIWI_ARCFU | O28951)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.

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Description

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Ligands, Modified Residues, Ions (2, 22)

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SS Bonds (0, 0)

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