1Z25 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF P.FURIOSUS ARGONAUTE WITH BOUND MN2+

Authors :   F. V. Rivas, N. H. Tolia, J. J. Song, J. P. Aragon, J. Liu, G. J. Hannon, L. Joshua-Tor

Date :   07 Mar 05 (Deposition) - 05 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A

Keywords :   Argonaute, Piwi, Active Site, Rnaseh, Mg2+, Rnai, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. V. Rivas, N. H. Tolia, J. J. Song, J. P. Aragon, J. Liu, G. J. Hannon, L. Joshua-Tor
Purified Argonaute2 And An Sirna Form Recombinant Human Risc.
Nat. Struct. Mol. Biol. V. 12 340 2005
PubMed-ID: 15800637 | Reference-DOI: 10.1038/NSMB918
(for further references see the PDB file header)

Molecule 1 - ARGONAUTE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSMT3
	Expression System Strain	:	BL21RIPL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:558 , ASP A:628 , HIS A:745 , HOH A:774 , HOH A:781 , HOH A:788	BINDING SITE FOR RESIDUE MN A 771

(no "SS Bond" information available for 1Z25)

(no "Cis Peptide Bond" information available for 1Z25)

(no "SAP(SNP)/Variant" information available for 1Z25)

(no "PROSITE Motif" information available for 1Z25)

(no "Exon" information available for 1Z25)

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:713
 aligned with Q8U3D2_PYRFU | Q8U3D2 from UniProtKB/TrEMBL  Length:770

    Alignment length:771
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769 
         Q8U3D2_PYRFU     - -MKAKVVINLVKINKKIIPDKIYVYRLFNDPEEELQKEGYSIYRLAYENVGIVIDPENLIIATTKELEYEGEFIPEGEISFSELRNDYQSKLVLRLLKENGIGEYELSKLLRKFRKPKTFGDYKVIPSVEMSVIKHDEDFYLVIHIIHQIQSMKTLWELVNKDPKELEEFLMTHKENLMLKDIASPLKTVYKPCFEEYTKKPKLDHNQEIVKYWYNYHIERYWNTPEAKLEFYRKFGQVDLKQPAILAKFASKIKKNKNYKIYLLPQLVVPTYNAEQLESDVAKEILEYTKLMPEERKELLENILAEVDSDIIDKSLSEIEVEKIAQELENKIRVRDDKGNSVPISQLNVQKSQLLLWTNYSRKYPVILPYEVPEKFRKIREIPMFIILDSGLLADIQNFATNEFRELVKSMYYSLAKKYNSLAKKARSTNEIGLPFLDFRGKEKVITEDLNSDKGIIEVVEQVSSFMKGKELGLAFIAARNKLSSEKFEEIKRRLFNLNVISQVVNEDTLKNKRDKYDRNRLDLFVRHNLLFQVLSKLGVKYYVLDYRFNYDYIIGIDVAPMKRSEGYIGGSAVMFDSQGYIRKIVPIKIGEQRGESVDMNEFFKEMVDKFKEFNIKLDNKKILLLRDGRITNNEEEGLKYISEMFDIEVVTMDVIKNHPVRAFANMKMYFNLGGAIYLIPHKLKQAKGTPIPIKLAKKRIIKNGKVEKQSITRQDVLDIFILTRLNYGSISADMRLPAPVHYAHKFANAIRNEWKIKEEFLAEGFLYFV 770
               SCOP domains d1z25a1 A:0-323 Argonaute h            omologue PF0537                                                                                                                                                                                                                                                                              d1z25a2 A:324-770 Argon        aute homologue PF0537                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------PAZ_siRNAbind-1z25A02 A:155-201                --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Piwi-1z25A01 A:474-756                                                                                                                                                                                                                                                                     -------------- Pfam domains
         Sec.struct. author ..eeeee..eee.hhhhh...eeeee.------------.hhhhhhhhh.eeeee....eeee..........eeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee..eeeeeeeeeeeee....eeeeeeeeeeeee..hhhhhh..hhhhhhhhhhhh....eee........eeee..........ee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eeeeee...-----...eee.....eeeee....----...hhhhhh.hhhhhhhhhhhhhhhh..........eeeeee.hhhhhh.ee.............--------.hhhhhh...........hhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhhhh.-----------------------------.eeeee...hhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhh..eeeeeeehhhhhhhee..eeeeehhhhhhhhhhhhhhhh.....ee.......eeeeeeeeee......eeeeeeeee....eeeeeeee.........hhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhh.eeeeeeee............eeeee..eeeee.............eeeeeeeeee..eeee...hhhhhhhhhhhhh............hhhhhhhhhhhhhhhh....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z25 A   0 SMKAIVVINLVKINKKIIPDKIYVYRL------------YSIYRLAYENVGIVIDPENLIIATTKELEYEGEFIPEGEISFSELRNDYQSKLVLRLLKENGIGEYELSKLLRKFRKPKTFGDYKVIPSVEMSVIKHDEDFYLVIHIIHQIQSMKTLWELVNKDPKELEEFLMTHKENLMLKDIASPLKTVYKPCFEEYTKKPKLDHNQEIVKYWYNYHIERYWNTPEAKLEFYRKFGQVDLKQPAILAKFASK-----NYKIYLLPQLVVPTYNAEQL----AKEILEYTKLMPEERKELLENILAEVDSDIIDKSLSEIEVEKIAQELENKIRVRDDKGNSVPISQ--------LLWTNYSRKYPVILPYEVPEKFRKIREIPMFIILDSGLLADIQNFATNEFRELVKSMYY-----------------------------EKVITEDLNSDKGIIEVVEQVSSFMKGKELGLAFIAARNKLSSEKFEEIKRRLFNLNVISQVVNEDTLKNKRDKYDRNRLDLFVRHNLLFQVLSKLGVKYYVLDYRFNYDYIIGIDVAPMKRSEGYIGGSAVMFDSQGYIRKIVPIKIGEQRGESVDMNEFFKEMVDKFKEFNIKLDNKKILLLRDGRITNNEEEGLKYISEMFDIEVVTMDVIKNHPVRAFANMKMYFNLGGAIYLIPHKLKQAKGTPIPIKLAKKRIIKNGKVEKQSITRQDVLDIFILTRLNYGSISADMRLPAPVHYAHKFANAIRNEWKIKEEFLAEGFLYFV 770
                                     9        19      |  -        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  |    259       269       | -  |    289       299       309       319       329       339      |  -     | 359       369       379       389       399       409   |     -         -         -   |   449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769 
                                                     26           39                                                                                                                                                                                                                  252   258                277  282                                                             346      355                                                       413                           443

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: PAZ domain (15)

Family: PAZ domain (15)

Protein domain: Argonaute homologue PF0537 (3)

Pyrococcus furiosus [TaxId: 2261] (3)

d1z25a1

A:0-323

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: Argonaute homologue PF0537 (3)

Pyrococcus furiosus [TaxId: 2261] (3)

d1z25a2

A:324-770

(no "CATH Domain" information available for 1Z25)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q8U3D2_PYRFU | Q8U3D2)

molecular function
	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.

Asymmetric/Biological Unit
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	1z25
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	Q8U3D2_PYRFU \| Q8U3D2
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UniProtKB/TrEMBL
	Q8U3D2_PYRFU \| Q8U3D2	:	1u04 1z26

1u04	APO P.FURIOSUS ARGONAUTE
1z26	STRUCTURE OF PYROCOCCUS FURIOSUS ARGONAUTE WITH BOUND TUNGSTATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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