2W42 - 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 :   THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.

Authors :   J. S. Parker, S. M. Roe, D. Barford

Date :   19 Nov 08 (Deposition) - 09 Dec 08 (Release) - 17 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,P,Q,R,S
Biol. Unit 1: A,P,Q  (1x)
Biol. Unit 2: B,R,S  (1x)

Keywords :   Rnai, Risc, Argonaute, Piwi Domain, Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Parker, E. A. Parizotto, M. Wang, S. M. Roe, D. Barford
Enhancement Of The Seed-Target Recognition Step In Rna Silencing By A Piwi-Mid Domain Protein
Mol. Cell V. 33 204 2009
PubMed-ID: 19187762 | Reference-DOI: 10.1016/J.MOLCEL.2008.12.012

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-17B
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	PIWI

*Molecule 2 - 5'-D(TPTPCPGPAPCPGPCP)-3'*
	Chains	:	P, R
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

*Molecule 3 - 5'-D(GPTPCPGPAPAPTPTP)-3'*
	Chains	:	Q, S
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	P	Q	R	S
Biological Unit 1 (1x)	:	A		P	Q
Biological Unit 2 (1x)	:		B			R	S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:159 , LEU A:427 , HOH A:2244 , DT P:1 , DC P:3	BINDING SITE FOR RESIDUE MN A1428
2	AC2	SOFTWARE	GLN B:159 , LEU B:427 , HOH B:2143 , DT R:1 , DC R:3	BINDING SITE FOR RESIDUE MN B1428

(no "SS Bond" information available for 2W42)

(no "Cis Peptide Bond" information available for 2W42)

(no "SAP(SNP)/Variant" information available for 2W42)

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 2W42)

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:395
 aligned with PIWI_ARCFU | O28951 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:417
                                    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    11 LTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w42A01 A:11-172  [code=3.40.50.2300, no name defined]                                                                                                            2w42A02 A:173-427  [code=3.30.420.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh.eee..hhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeee.hhh...hhhhhhhhhhhhhhhhh.....ee.........eeeeeeeee....eeeeeeeee.....eeeeee...ee..hhhhhhhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee........--------...................---------.eeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.....-----hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------PIWI  PDB: A:110-406 UniProt: 110-406                                                                                                                                                                                                                                                                    --------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w42 A  11 LTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMG--------YEGTKVKLSSKRYLLTLLQ---------MVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPI-----RSLQTNPWFL 427
                                    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 |       -|      320        |-       340       350       360       370       380       390       400       410 |     420       
                                                                                                                                                                                                                                                                                                                             302      311               329       339                                                                      412   418

Chain B from PDB  Type:PROTEIN  Length:389
 aligned with PIWI_ARCFU | O28951 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:417
                                    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    11 LTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w42B01 B:11-172  [code=3.40.50.2300, no name defined]                                                                                                            2w42B02 B:173-427  [code=3.30.420.10, no name defined]                                                                                                                                                                                                          CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------Piwi-2w42B01 B:110-406                                                                                                                                                                                                                                                                                   ------      --------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------Piwi-2w42B02 B:110-406                                                                                                                                                                                                                                                                                   ------      --------- Pfam domains (2)
         Sec.struct. author .eee.hhh.eee..hhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeee...----.hhhhhhhhhhhhhhhh.....ee.........eeeeeeeee....eeeeeeeee.....eeeeee...ee..hhhhhhhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee........--------...................----------.eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....------......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------PIWI  PDB: B:110-406 UniProt: 110-406                                                                                                                                                                                                                                                                    --------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w42 B  11 LTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDI----NLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMG--------YEGTKVKLSSKRYLLTLLQ----------VTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPI------SLQTNPWFL 427
                                    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 |       -|      320        |-       340       350       360       370       380       390       400       410 |     420       
                                                                                                                                                              143  148                                                                                                                                                       302      311               329        340                                                                     412    419

Chain P from PDB  Type:DNA  Length:6
                                      
                 2w42 P   1 TTCGAC   6

Chain Q from PDB  Type:DNA  Length:6
                                      
                 2w42 Q   9 GTCGAA  14

Chain R from PDB  Type:DNA  Length:6
                                      
                 2w42 R   1 TTCGAC   6

Chain S from PDB  Type:DNA  Length:4
                                    
                 2w42 S  11 CGAA  14

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 2W42)

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)

Archaeoglobus fulgidus. Organism_taxid: 2234. (3)

1a	2w42B02	B:173-427
1b	2w42A02	A:173-427

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

Topology: Rossmann fold (7312)

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

Archaeoglobus fulgidus. Organism_taxid: 2234. (3)

2a	2w42B01	B:11-172
2b	2w42A01	A:11-172

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-2w42B01	B:110-406
1b	Piwi-2w42B02	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w42)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2w42
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PIWI_ARCFU \| O28951
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PIWI_ARCFU \| O28951
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PIWI_ARCFU \| O28951	:	1w9h 1ytu 2bgg

1w9h	THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS.
2bgg	THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT SIRNA DUPLEX.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File