2I91 | PR0232 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   60KDA RO AUTOANTIGEN IN COMPLEX WITH A FRAGMENT OF MISFOLDED RNA

Authors :   K. M. Reinisch, A. J. Stein

Date :   04 Sep 06 (Deposition) - 17 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   Von Willebrand Factor A, Rossmann-Fold, Heat Repeat, Midas Motif, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Fuchs, A. J. Stein, C. Fu, K. M. Reinisch, S. L. Wolin
Structural And Biochemical Basis For Misfolded Rna Recognition By The Ro Autoantigen.
Nat. Struct. Mol. Biol. V. 13 1002 2006
PubMed-ID: 17041599 | Reference-DOI: 10.1038/NSMB1156
(for further references see the PDB file header)

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

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

Molecule 3 - 60 KDA SS-A/RO RIBONUCLEOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TROVE2
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	60 KDA RO PROTEIN, 60 KDA RIBONUCLEOPROTEIN RO, RORNP, TROVE DOMAIN FAMILY MEMBER 2

		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, 4)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:47 , SER A:378 , ALA A:379 , SER A:380 , GLY A:443 , SER A:444 , THR A:445 , ASN A:473 , MG A:701	BINDING SITE FOR RESIDUE ACT A 601
2	AC2	SOFTWARE	TYR B:47 , SER B:378 , ALA B:379 , SER B:380 , GLY B:443 , SER B:444 , THR B:445 , ASN B:473 , MG B:702 , HOH B:806	BINDING SITE FOR RESIDUE ACT B 602
3	AC3	SOFTWARE	SER A:378 , SER A:380 , THR A:445 , ACT A:601 , HOH A:702 , HOH A:915	BINDING SITE FOR RESIDUE MG A 701
4	AC4	SOFTWARE	SER B:378 , SER B:380 , THR B:445 , ACT B:602 , HOH B:703 , HOH B:806	BINDING SITE FOR RESIDUE MG B 702

(no "SS Bond" information available for 2I91)

(no "Cis Peptide Bond" information available for 2I91)

(no "SAP(SNP)/Variant" information available for 2I91)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TROVE	PS50988	TROVE domain profile.	RO60_XENLA	16-369	2	A:16-369 B:16-369

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TROVE	PS50988	TROVE domain profile.	RO60_XENLA	16-369	1	A:16-369 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TROVE	PS50988	TROVE domain profile.	RO60_XENLA	16-369	1	- B:16-369

(no "Exon" information available for 2I91)

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:520
 aligned with RO60_XENLA | P42700 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:533
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   
           RO60_XENLA     5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
               SCOP domains d2i91a1 A:5-363 60-kda SS-aARo ribonucleoprotein                                                                                                                                                                                                                                                                                                                       d2i91a2 A:364-537 60-kda SS-A/Ro ribonucleoprotein, RoRNP                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.....eeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh--------.hhhhhhhhhhhhhh.hhhhhhhhhhhh.ee..eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh-----hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..........eeeeee.hhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee...ee........hhhhhhhhhhhhh......hhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhh...eeeeee.....ee........eeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------TROVE  PDB: A:16-369 UniProt: 16-369                                                                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i91 A   5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDL--------WGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAY-----SPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
                                    14        24        34        44        54        64        74        84        94       104       114       124       134|      144       154       164       174       184       194       204        |-    |  224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   
                                                                                                                                                            135      144                                                                  213   219

Chain B from PDB  Type:PROTEIN  Length:526
 aligned with RO60_XENLA | P42700 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:533
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   
           RO60_XENLA     5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
               SCOP domains d2i91b1 B:5-363 60-kda SS-aARo ribonucleoprotein                                                                                                                                                                                                                                                                                                                       d2i91b2 B:364-537 60-kda SS-A/Ro ribonucleoprotein, RoRNP                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.....eeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh-------.hhhhhhhhhhhhhh.hhhhhhhhhhhh.ee..eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..........eeeeee.hhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee...ee........hhhhhhhhhhhhh......hhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhh...eeeeee.....ee........eeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------TROVE  PDB: B:16-369 UniProt: 16-369                                                                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i91 B   5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLK-------WGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
                                    14        24        34        44        54        64        74        84        94       104       114       124       134 |     144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   
                                                                                                                                                             136     144

Chain C from PDB  Type:RNA  Length:8
                                        
                 2i91 C   1 GCCUACCC   8

Chain D from PDB  Type:RNA  Length:14
                                              
                 2i91 D   2 GGUAGGCUUUUCAA  15
                                    11

Chain E from PDB  Type:RNA  Length:8
                                        
                 2i91 E   1 GCCUACCC   8

Chain F from PDB  Type:RNA  Length:15
                                               
                 2i91 F   1 CGGUAGGCUUUUCAA  15
                                    10

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 "CATH Domain" information available for 2I91)

(no "Pfam Domain" information available for 2I91)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RO60_XENLA | P42700)

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:0034336	misfolded RNA binding	Interacting selectively and non-covalently with an RNA molecule that has assumed an incorrect conformation.
biological process
	GO:0030030	cell projection organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2i91)

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

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	2i91
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	RO60_XENLA \| P42700	:	1yvp 1yvr

(no "Related Entries Specified in the PDB File" available for 2I91)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

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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