2VOD - JenaLib

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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER AUAUUUU

Authors :   O. Kotik-Kogan, E. R. Valentine, D. Sanfelice, M. R. Conte, S. Curry

Date :   15 Feb 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Rna Recognition Motif, Systemic Lupus Erythematosus, Phosphoprotein, Rna Maturation, Rna-Binding Protein, Nucleus, La Motif, Rna-Binding, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Kotik-Kogan, E. R. Valentine, D. Sanfelice, M. R. Conte, S. Curry
Structural Analysis Reveals Conformational Plasticity In The Recognition Of Rna 3' Ends By The Human La Protein.
Structure V. 16 852 2008
PubMed-ID: 18547518 | Reference-DOI: 10.1016/J.STR.2008.02.021

Molecule 1 - LUPUS LA PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 4-194
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HUMAN LA PROTEIN, SJOEGREN SYNDROME TYPE B ANTIGEN, SS-B, LA RIBONUCLEOPROTEIN, LA AUTOANTIGEN

*Molecule 2 - 5'-R(APUPAPUPUPUPUP)-3'**
	Chains	:	C, D
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2VOD)

(no "Site" information available for 2VOD)

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034066	P	48	S	LA_HUMAN	Polymorphism	17160793	A/B	P	48	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034066	P	48	S	LA_HUMAN	Polymorphism	17160793	A	P	48	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034066	P	48	S	LA_HUMAN	Polymorphism	17160793	B	P	48	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LA	PS50961	La-type HTH domain profile.	LA_HUMAN	7-99	2	A:7-99 B:7-99
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	LA_HUMAN	111-187	2	A:111-187 B:111-187

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LA	PS50961	La-type HTH domain profile.	LA_HUMAN	7-99	1	A:7-99 -
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	LA_HUMAN	111-187	1	A:111-187 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LA	PS50961	La-type HTH domain profile.	LA_HUMAN	7-99	1	- B:7-99
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	LA_HUMAN	111-187	1	- B:111-187

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000260956	2a	ENSE00001893329	chr2:170655322-170655486	165	LA_HUMAN	-	0	0	-	-
1.4	ENST00000260956	4	ENSE00002156069	chr2:170657462-170657536	75	LA_HUMAN	1-22	22	2	A:6-22 B:5-22	17 18
1.5	ENST00000260956	5	ENSE00001610086	chr2:170661984-170662087	104	LA_HUMAN	23-57	35	2	A:23-57 B:23-57	35 35
1.6a	ENST00000260956	6a	ENSE00000782038	chr2:170662175-170662349	175	LA_HUMAN	57-115	59	2	A:57-115 B:57-115	59 59
1.7c	ENST00000260956	7c	ENSE00000782039	chr2:170663295-170663402	108	LA_HUMAN	116-151	36	2	A:116-151 B:116-151	36 36
1.7g	ENST00000260956	7g	ENSE00002168098	chr2:170663481-170663581	101	LA_HUMAN	152-185	34	2	A:152-185 B:152-185	34 34
1.8c	ENST00000260956	8c	ENSE00000782041	chr2:170664992-170665063	72	LA_HUMAN	185-209	25	2	A:185-192 B:185-192	8 8
1.8e	ENST00000260956	8e	ENSE00000782042	chr2:170665370-170665412	43	LA_HUMAN	209-223	15	0	-	-
1.9c	ENST00000260956	9c	ENSE00000782043	chr2:170666793-170666933	141	LA_HUMAN	224-270	47	0	-	-
1.10b	ENST00000260956	10b	ENSE00000782044	chr2:170667368-170667554	187	LA_HUMAN	271-333	63	0	-	-
1.11	ENST00000260956	11	ENSE00000782045	chr2:170667693-170667833	141	LA_HUMAN	333-380	48	0	-	-
1.12b	ENST00000260956	12b	ENSE00001588653	chr2:170668178-170668574	397	LA_HUMAN	380-408	29	0	-	-

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:187
 aligned with LA_HUMAN | P05455 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:187
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       
             LA_HUMAN     6 DNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAKK 192
               SCOP domains d2voda1 A:6-103 Lupus La autoantigen N-terminal domain                                            -d2voda2 A:105-192 Lupus LA protein                                                       SCOP domains
               CATH domains 2vodA01 A:6-90 'winged helix' repressor DNA binding domain                           ---------2vodA02 A:100-192  [code=3.30.70.330, no name defined]                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eehhhhh.hhhhhhhh.hhhhhhhhhhhh....eee.....eeee.........hhhhhhhhhh.eeeee......hhhhhhhhhh....eeeeeeee.....eeeeeeeee.hhhhhhhhhhh..........eeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -HTH_LA  PDB: A:7-99 UniProt: 7-99                                                            -----------RRM  PDB: A:111-187 UniProt: 111-187                                         ----- PROSITE
           Transcript 1 (1) Exon 1.4         Exon 1.5  PDB: A:23-57             ----------------------------------------------------------Exon 1.7c  PDB: A:116-151           Exon 1.7g  PDB: A:152-185         ------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.6a  PDB: A:57-115 UniProt: 57-115                   ---------------------------------------------------------------------1.8c     Transcript 1 (2)
                 2vod A   6 DNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAKK 192
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with LA_HUMAN | P05455 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184        
             LA_HUMAN     5 GDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAKK 192
               SCOP domains -d2vodb1 B:6-103 Lupus La autoantigen N-terminal domain                                            -d2vodb2 B:105-192 Lupus LA protein                                                       SCOP domains
               CATH domains 2vodB01 B:5-90 'winged helix' repressor DNA binding domain                            ---------2vodB02 B:100-192  [code=3.30.70.330, no name defined]                                        CATH domains
           Pfam domains (1) ------------La-2vodB03 B:17-75                                         -------------------------------------RRM_1-2vodB01 B:113-181                                              ----------- Pfam domains (1)
           Pfam domains (2) ------------La-2vodB04 B:17-75                                         -------------------------------------RRM_1-2vodB02 B:113-181                                              ----------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eehhhhh.hhhhhhhh.hhhhhhhhh.......eee.....eeee.........hhhhhhhhhhheeeee......hhhhhhhhhh....eeeeeeee.....eeeeeeeee.hhhhhhhhhhh...ee..ee.eeeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --HTH_LA  PDB: B:7-99 UniProt: 7-99                                                            -----------RRM  PDB: B:111-187 UniProt: 111-187                                         ----- PROSITE
           Transcript 1 (1) Exon 1.4          Exon 1.5  PDB: B:23-57             ----------------------------------------------------------Exon 1.7c  PDB: B:116-151           Exon 1.7g  PDB: B:152-185         ------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.6a  PDB: B:57-115 UniProt: 57-115                   ---------------------------------------------------------------------1.8c     Transcript 1 (2)
                 2vod B   5 GDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAKK 192
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain C from PDB  Type:RNA  Length:7
                                       
                 2vod C  -7 AUAUUUU  -1

Chain D from PDB  Type:RNA  Length:7
                                       
                 2vod D  -7 AUAUUUU  -1

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: La domain (9)

Protein domain: Lupus La autoantigen N-terminal domain (8)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d2voda1	A:6-103
1b	d2vodb1	B:6-103

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: Lupus LA protein (8)

Human (Homo sapiens) [TaxId: 9606] (8)

2a	d2voda2	A:105-192
2b	d2vodb2	B:105-192

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

Human (Homo sapiens) (81)

1a	2vodA02	A:100-192
1b	2vodB02	B:100-192

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Human (Homo sapiens) (70)

2a	2vodA01	A:6-90
2b	2vodB01	B:5-90

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Homo sapiens (Human) (94)

1a	RRM_1-2vodB01	B:113-181
1b	RRM_1-2vodB02	B:113-181

Clan: no clan defined [family: La] (7)

Family: La (7)

Homo sapiens (Human) (6)

2a	La-2vodB03	B:17-75
2b	La-2vodB04	B:17-75

Asymmetric Unit(hide GO term definitions)

Chain A,B (LA_HUMAN | P05455)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0075522	IRES-dependent viral translational initiation	Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0008334	histone mRNA metabolic process	The chemical reactions and pathways involving an mRNA encoding a histone.
	GO:1903608	protein localization to cytoplasmic stress granule	A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
	GO:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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	2vod
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UniProtKB/Swiss-Prot
	LA_HUMAN \| P05455	:	1owx 1s79 1s7a 1yty 1zh5 2von 2voo 2vop

1owx	SOLUTION STRUCTURE OF THE C-TERMINAL RRM OF HUMAN LA (LA225-334)
1s79	SOLUTION STRUCTURE OF THE CENTRAL RRM OF HUMAN LA PROTEIN
1s7a	NMR STRUCTURE OF THE LA MOTIF OF HUMAN LA PROTEIN
1yty	STRUCTURAL BASIS FOR RECOGNITION OF UUUOH 3 '-TERMINII OFNASCENT RNA POL III TRANSCRIPTS BY LA AUTOANTIGEN
1zh5	STRUCTURAL BASIS FOR RECOGNITION OF UUUOH 3 '-TERMINII OFNASCENT RNA POL III TRANSCRIPTS BY LA AUTOANTIGEN
2von	CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER AUAUUUU
2voo	CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER UUUUUUUU
2vop	CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER AUUUU

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