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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   THE STRUCTURE OF THE ZINC FINGER FROM THE HUMAN SPLICEOSOMAL PROTEIN U1C

Authors :   Y. Muto, D. Pomeranz-Krummel, C. Oubridge, H. Hernandez, C. Robinson, D. Neuhaus, K. Nagai

Date :   31 Mar 08 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (47x)

Keywords :   Rna-Binding Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Spliceosomal Protein, Phosphoprotein, Nuclear Protein, Ribonucleoprotein, Zinc-Finger, Zinc Finger, Metal-Binding, Zinc, Rsgi, Nucleus, U1 Snrnp, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Muto, D. Pomeranz-Krummel, C. Oubridge, H. Hernandez, C. Robinson, D. Neuhaus, K. Nagai
The Structure And Biochemical Properties Of The Human Spliceosomal Protein U1C
J. Mol. Biol. V. 341 185 2004
PubMed-ID: 15312772 | Reference-DOI: 10.1016/J.JMB.2004.04.078

Molecule 1 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Fragment	:	ZINC FINGER DOMAIN, RESIDUES 1-61
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U1 SNRNP PROTEIN C, U1C PROTEIN, U1-C


NMR Structure (47x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:6 , CYS A:9 , HIS A:24 , HIS A:30	BINDING SITE FOR RESIDUE ZN A1062

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_MATRIN	PS50171	Zinc finger matrin-type profile.	RU1C_HUMAN	4-36	1	A:4-36

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000244520	1a	ENSE00001462178	chr6:34725183-34725328	146	RU1C_HUMAN	1-3	3	1	A:1-3	3
1.2b	ENST00000244520	2b	ENSE00002200647	chr6:34725689-34725731	43	RU1C_HUMAN	3-17	15	1	A:3-17	15
1.3	ENST00000244520	3	ENSE00002143688	chr6:34730372-34730480	109	RU1C_HUMAN	18-54	37	1	A:18-54	37
1.4	ENST00000244520	4	ENSE00002143039	chr6:34735685-34735774	90	RU1C_HUMAN	54-84	31	1	A:54-61	8
1.5	ENST00000244520	5	ENSE00002151467	chr6:34738068-34738172	105	RU1C_HUMAN	84-119	36	0	-	-
1.7c	ENST00000244520	7c	ENSE00001196088	chr6:34741223-34741571	349	RU1C_HUMAN	119-159	41	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:61
 aligned with RU1C_HUMAN | P09234 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:61
                                    10        20        30        40        50        60 
            RU1C_HUMAN    1 MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGK 61
               SCOP domains d2vrda1 A:1-61 Spliceosomal protein U1C                       SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains zf-U1-2vrdA01 A:1-38                  ----------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhh..hhhhhhhhhhh.........hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZF_MATRIN  PDB: A:4-36           ------------------------- PROSITE
           Transcript 1 (1) 1.1--------------Exon 1.3  PDB: A:18-54 UniProt: 18-54------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2b      ------------------------------------Exon 1.4 Transcript 1 (2)
                  2vrd A  1 MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGK 61
                                    10        20        30        40        50        60

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: beta-beta-alpha zinc fingers (183)

Superfamily: beta-beta-alpha zinc fingers (183)

Family: HkH motif-containing C2H2 finger (4)

Protein domain: Spliceosomal protein U1C (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2vrda1

A:1-61

(no "CATH Domain" information available for 2VRD)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C2H2-zf (71)

Family: zf-U1 (1)

Homo sapiens (Human) (1)

zf-U1-2vrdA01

A:1-38

NMR Structure(hide GO term definitions)

Chain A (RU1C_HUMAN | P09234)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0030619	U1 snRNA binding	Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA).
	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: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.
	GO:0030627	pre-mRNA 5'-splice site binding	Interacting selectively and non-covalently with the pre-mRNA 5' splice site sequence.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0000395	mRNA 5'-splice site recognition	Recognition of the intron 5'-splice site by components of the assembling spliceosome.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	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:0005685	U1 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U1.
	GO:0071004	U2-type prespliceosome	A spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation.
	GO:0000243	commitment complex	A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript.
	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:0071010	prespliceosome	A spliceosomal complex that is formed by association of the 5' splice site and the branch point sequence with specific snRNPs. The prespliceosome includes many proteins in addition to those found in the bound snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation. Prespliceosome complexes are not active for splicing, but are instead an early step in the assembly of a spliceosomal complex.

NMR Structure
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Description

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Ligands, Modified Residues, Ions (1, 1)

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Exons (4, 4)

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