1YVP | PR0151 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

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 :   RO AUTOANTIGEN COMPLEXED WITH RNAS

Authors :   A. J. Stein, G. Fuchs, C. Fu, S. L. Wolin, K. M. Reinisch

Date :   16 Feb 05 (Deposition) - 07 Jun 05 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   A. J. Stein, G. Fuchs, C. Fu, S. L. Wolin, K. M. Reinisch
Structural Insights Into Rna Quality Control: The Ro Autoantigen Binds Misfolded Rnas Via Its Central Cavity
Cell(Cambridge, Mass. ) V. 121 529 2005
PubMed-ID: 15907467 | Reference-DOI: 10.1016/J.CELL.2005.03.009

Molecule 1 - Y RNA SEQUENCE, FIRST STRAND
	Chains	:	C, E, G, H
	Engineered	:	YES
	Other Details	:	CHAINS G AND H ARE SINGLE STRANDS BOUND BY PROTEIN
	Synthetic	:	YES

Molecule 2 - Y RNA SEQUENCE, SECOND STRAND
	Chains	:	D, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - 60-KDA SS-A/RO RIBONUCLEOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	TN5 B1-4
	Expression System Common	:	CABBAGE LOOPER
	Expression System Organ	:	EGGS
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Other Details	:	PROTEIN A BINDS RNA CHAIN G, B BINDS H
	Synonym	:	RO AUTOANTIGEN

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A		C	D			G
Biological Unit 2 (1x)	:		B			E	F		H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	IU	8	Mod. Residue	5-IODOURIDINE-5'-MONOPHOSPHATE
3	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	IU	-1	Mod. Residue	5-IODOURIDINE-5'-MONOPHOSPHATE
3	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	IU	-1	Mod. Residue	5-IODOURIDINE-5'-MONOPHOSPHATE
3	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:1001	BINDING SITE FOR RESIDUE ACT A 2001
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:1002 , HOH B:2072	BINDING SITE FOR RESIDUE ACT B 2002
3	AC3	SOFTWARE	SER A:378 , SER A:380 , THR A:445 , ACT A:2001 , HOH A:2167 , HOH A:2168	BINDING SITE FOR RESIDUE MG A 1001
4	AC4	SOFTWARE	SER B:378 , SER B:380 , THR B:445 , ACT B:2002 , HOH B:2170 , HOH B:2171	BINDING SITE FOR RESIDUE MG B 1002

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

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

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

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 1YVP)

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:529
 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 d1yvpa1 A:5-363 60-kda SS-aARo ribonucleoprotein                                                                                                                                                                                                                                                                                                                       d1yvpa2 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.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhh.ee..eehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..----.....hhhhhhhhhhhhhhhh.........eeeeee.hhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee...ee........hhhhhhhh...........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
                 1yvp A   5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHG----LRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 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   
                                                                                                                                                                                                                                                                                                                                                                     336  341

Chain B from PDB  Type:PROTEIN  Length:532
 aligned with RO60_XENLA | P42700 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:534
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533    
           RO60_XENLA     4 TMDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
               SCOP domains d1yvpb1 B:4-363 60-kda SS-aARo ribonucleoprotein                                                                                                                                                                                                                                                                                                                        d1yvpb2 B:364-537 60-kda SS-A/Ro ribonucleoprotein, RoRNP                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------TROVE-1yvpB01 B:16-369                                                                                                                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------TROVE-1yvpB02 B:16-369                                                                                                                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ............ee.....eeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhh.ee..eehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...--......hhhhhhhhhhhhhhh..........eeeeee.hhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee...ee........hhhhhhhhhh.........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
                 1yvp B   4 TMDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGN--KLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333   |  |343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533    
                                                                                                                                                                                                                                                                                                                                                                       337  |                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                          340

Chain C from PDB  Type:RNA  Length:10
                                          
                 1yvp C   1 GCuGGUCCGA  10
                              |     10
                              3-IU

Chain D from PDB  Type:RNA  Length:10
                                          
                 1yvp D   1 uuGACuAGCC  10
                            ||   |  10
                            1-IU |    
                             2-IU|    
                                 6-IU

Chain E from PDB  Type:RNA  Length:10
                                          
                 1yvp E   1 GCuGGUCCGA  10
                              |     10
                              3-IU

Chain F from PDB  Type:RNA  Length:10
                                          
                 1yvp F   1 uuGACuAGCC  10
                            ||   |  10
                            1-IU |    
                             2-IU|    
                                 6-IU

Chain G from PDB  Type:RNA  Length:5
                                     
                 1yvp G   6 UCCGA  10

Chain H from PDB  Type:RNA  Length:7
                                       
                 1yvp H   4 GGUCCGA  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 1YVP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: TROVE] (3)

Family: TROVE (3)

Xenopus laevis (African clawed frog) (2)

1a	TROVE-1yvpB01	B:16-369
1b	TROVE-1yvpB02	B:16-369

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 1yvp)

Biological Units
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	1yvp
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	RO60_XENLA \| P42700	:	1yvr 2i91

1yvr	RO AUTOANTIGEN, NO RNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (4, 4)

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

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SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (1, 2)

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