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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF SMN TUDOR DOMAIN IN COMPLEX WITH SYMMETRICALLY DIMETHYLATED ARGININE

Authors :   K. Tripsianes, T. Madl, M. Machyna, D. Fessas, C. Englbrecht, U. Fische K. M. Neugebauer, M. Sattler

Date :   12 Oct 11 (Deposition) - 30 Nov 11 (Release) - 28 Dec 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tripsianes, T. Madl, M. Machyna, D. Fessas, C. Englbrecht, U. Fischer, K. M. Neugebauer, M. Sattler
Structural Basis For Dimethyl-Arginine Recognition By The Tudor Domains Of Human Smn And Spf30 Proteins
Nat. Struct. Mol. Biol. V. 18 1414 2011
PubMed-ID: 22101937 | Reference-DOI: 10.1038/NSMB.2185

Molecule 1 - SURVIVAL MOTOR NEURON PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	TUDOR DOMAIN, RESIDUES 84-147
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SURVIVAL MOTOR NEURON PROTEIN SMN, COMPONENT OF GEMS 1, GEMIN-1

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	2MR	1	Ligand/Ion	N3, N4-DIMETHYLARGININE

NMR Structure * (1, 1)

No.	Name	Count	Type	Full Name
1	2MR	1	Ligand/Ion	N3, N4-DIMETHYLARGININE

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:102 , ASP A:105 , TYR A:109 , TYR A:127 , TYR A:130 , ASN A:132	BINDING SITE FOR RESIDUE 2MR A1148

(no "SS Bond" information available for 4A4E)

(no "Cis Peptide Bond" information available for 4A4E)

NMR Structure (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034805	G	95	R	SMN_HUMAN	Disease (SMA3)	104893927	A	G	95	R
2	UniProt	VAR_034806	A	111	G	SMN_HUMAN	Disease (SMA2)	104893935	A	A	111	G
3	UniProt	VAR_034807	I	116	F	SMN_HUMAN	Disease (SMA1)	104893933	A	I	116	F
4	UniProt	VAR_034808	Q	136	E	SMN_HUMAN	Disease (SMA1)	104893934	A	Q	136	E

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

NMR Structure * (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034805	G	95	R	SMN_HUMAN	Disease (SMA3)	104893927	A	G	95	R
2	UniProt	VAR_034806	A	111	G	SMN_HUMAN	Disease (SMA2)	104893935	A	A	111	G
3	UniProt	VAR_034807	I	116	F	SMN_HUMAN	Disease (SMA1)	104893933	A	I	116	F
4	UniProt	VAR_034808	Q	136	E	SMN_HUMAN	Disease (SMA1)	104893934	A	Q	136	E

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUDOR	PS50304	Tudor domain profile.	SMN_HUMAN	91-151	1	A:91-147

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUDOR	PS50304	Tudor domain profile.	SMN_HUMAN	91-151	1	A:91-147

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000380743	1b	ENSE00001904512	chr5:69345439-69345593	155	SMN_HUMAN	1-27	27	0	-	-
1.2b	ENST00000380743	2b	ENSE00001725187	chr5:69359242-69359313	72	SMN_HUMAN	28-51	24	0	-	-
1.3	ENST00000380743	3	ENSE00001607984	chr5:69361792-69361911	120	SMN_HUMAN	52-91	40	1	A:84-91	8
1.4a	ENST00000380743	4a	ENSE00001656721	chr5:69362761-69362961	201	SMN_HUMAN	92-158	67	1	A:92-147	56
1.5b	ENST00000380743	5b	ENSE00001749658	chr5:69363121-69363273	153	SMN_HUMAN	159-209	51	0	-	-
1.7b	ENST00000380743	7b	ENSE00001651294	chr5:69365062-69365157	96	SMN_HUMAN	210-241	32	0	-	-
1.8a	ENST00000380743	8a	ENSE00001730323	chr5:69366468-69366578	111	SMN_HUMAN	242-278	37	0	-	-
1.10a	ENST00000380743	10a	ENSE00001755872	chr5:69372348-69372401	54	SMN_HUMAN	279-294	16	0	-	-
1.11c	ENST00000380743	11c	ENSE00001812360	chr5:69372846-69373419	574	SMN_HUMAN	-	0	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:64
 aligned with SMN_HUMAN | Q16637 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:64
                                    93       103       113       123       133       143    
            SMN_HUMAN    84 NTAASLQQWKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICE 147
               SCOP domains d4a4ea_ A: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee......eeeeeeeeee....eeeeee.....eeeee.hhh...... Sec.struct. author
                 SAPs(SNPs) -----------R---------------G----F-------------------E----------- SAPs(SNPs)
                    PROSITE -------TUDOR  PDB: A:91-147 UniProt: 91-151                      PROSITE
               Transcript 1 Exon 1.3Exon 1.4a  PDB: A:92-147 UniProt: 92-158 [INCOMPLETE]    Transcript 1
                 4a4e A  84 NTAASLQQWKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICE 147
                                    93       103       113       123       133       143

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 '\|'

NMR Structure

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: Tudor domain (24)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d4a4ea_

(no "CATH Domain" information available for 4A4E)

(no "Pfam Domain" information available for 4A4E)

NMR Structure(hide GO term definitions)

Chain A (SMN_HUMAN | Q16637)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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).
biological process
	GO:0006353	DNA-templated transcription, termination	The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0051170	nuclear import	The directed movement of substances into the nucleus.
	GO:0000245	spliceosomal complex assembly	The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
	GO:0000387	spliceosomal snRNP assembly	The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
cellular component
	GO:0015030	Cajal body	A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
	GO:0097504	Gemini of coiled bodies	Nuclear bodies frequently found near or associated with Cajal bodies (also called coiled bodies or CBs). Gemini of coiled bodies, or 'gems', are similar in size and shape to CBs, and often indistinguishable under the microscope. Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs); they contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis, and to play a role in the etiology of spinal muscular atrophy (SMA).
	GO:0032797	SMN complex	A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
	GO:0034719	SMN-Sm protein complex	A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm.
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0036464	cytoplasmic ribonucleoprotein granule	A ribonucleoprotein granule located in the cytoplasm.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.
	GO:0043204	perikaryon	The portion of the cell soma (neuronal cell body) that excludes the nucleus.

NMR Structure
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	SMN_HUMAN \| Q16637	:	1g5v 1mhn 2leh 3s6n 4a4g 4gli 4qq6 5mf9

1g5v	SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF THE HUMAN SMNPROTEIN
1mhn	HIGH RESOLUTION CRYSTAL STRUCTURE OF THE SMN TUDOR DOMAIN
4a4f	SOLUTION STRUCTURE OF SPF30 TUDOR DOMAIN IN COMPLEX WITH SYMMETRICALLY DIMETHYLATED ARGININE
4a4g	SOLUTION STRUCTURE OF SMN TUDOR DOMAIN IN COMPLEX WITH ASYMMETRICALLY DIMETHYLATED ARGININE
4a4h	SOLUTION STRUCTURE OF SPF30 TUDOR DOMAIN IN COMPLEX WITH ASYMMETRICALLY DIMETHYLATED ARGININE

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

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Sequence-Structure Mapping

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Exons (2, 2)

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Gene Ontology (22, 22)

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