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NMR Structure - model 1

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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   SOLUTION NMR STRUCTURE OF CAPER RRM2 DOMAIN. NORTHEAST STRUCTURAL GENOMICS TARGET HR4730A

Authors :   P. Rossi, L. Zhao, C. Nwosu, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, G. Swapna, T. B. Acton, B. Rost, G. T. Montelione, Northeast Structural Genomics Consortium (Nesg)

Date :   28 Jun 07 (Deposition) - 04 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Rna Binding Motif Of Rbm39_human (Caper), Rrm2 Domain, Solution Nmr Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Rossi, R. Xiao, T. B. Acton, G. T. Montelione
Solution Nmr Structure Of Caper Rrm2 Domain.
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - RNA-BINDING PROTEIN 39
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector	:	HR4730A-15.1
	Expression System Vector Type	:	PLASMID
	Fragment	:	RRM2 DOMAIN: RESIDUES 235-331
	Gene	:	RBM39, HCC1, RNPC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNA-BINDING MOTIF PROTEIN 39, RNA-BINDING REGION- CONTAINING PROTEIN 2, HEPATOCELLULAR CARCINOMA PROTEIN 1, SPLICING FACTOR HCC1

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2JRS)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM39_HUMAN	250-328 153-230	1	A:27-105 -

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1q	ENST00000253363	1q	ENSE00001938005	chr20:34329873-34329863	11	RBM39_HUMAN	-	0	0	-	-
1.3a	ENST00000253363	3a	ENSE00002165663	chr20:34328809-34328746	64	RBM39_HUMAN	1-17	17	0	-	-
1.3m	ENST00000253363	3m	ENSE00001659166	chr20:34326939-34326890	50	RBM39_HUMAN	18-34	17	0	-	-
1.7e	ENST00000253363	7e	ENSE00002169946	chr20:34320057-34319863	195	RBM39_HUMAN	34-99	66	0	-	-
1.8c	ENST00000253363	8c	ENSE00001633700	chr20:34317449-34317384	66	RBM39_HUMAN	99-121	23	0	-	-
1.9a	ENST00000253363	9a	ENSE00001644239	chr20:34317287-34317234	54	RBM39_HUMAN	121-139	19	0	-	-
1.10c	ENST00000253363	10c	ENSE00001789378	chr20:34313077-34312960	118	RBM39_HUMAN	139-178	40	0	-	-
1.11c	ENST00000253363	11c	ENSE00002082263	chr20:34312644-34312492	153	RBM39_HUMAN	179-229	51	1	A:1-6 (gaps)	11
1.12b	ENST00000253363	12b	ENSE00001773401	chr20:34309799-34309662	138	RBM39_HUMAN	230-275	46	1	A:7-52	46
1.13a	ENST00000253363	13a	ENSE00001613700	chr20:34304727-34304662	66	RBM39_HUMAN	276-297	22	1	A:53-74	22
1.14a	ENST00000253363	14a	ENSE00001623326	chr20:34302311-34302107	205	RBM39_HUMAN	298-366	69	1	A:75-108	34
1.16e	ENST00000253363	16e	ENSE00001600583	chr20:34301018-34300941	78	RBM39_HUMAN	366-392	27	0	-	-
1.18b	ENST00000253363	18b	ENSE00001753743	chr20:34297196-34297146	51	RBM39_HUMAN	392-409	18	0	-	-
1.19d	ENST00000253363	19d	ENSE00001693917	chr20:34295123-34295042	82	RBM39_HUMAN	409-436	28	0	-	-
1.20c	ENST00000253363	20c	ENSE00001670308	chr20:34293252-34293147	106	RBM39_HUMAN	436-471	36	0	-	-
1.20f	ENST00000253363	20f	ENSE00001598280	chr20:34292668-34292590	79	RBM39_HUMAN	472-498	27	0	-	-
1.21h	ENST00000253363	21h	ENSE00001887140	chr20:34292503-34291532	972	RBM39_HUMAN	498-530	33	0	-	-

Sequences/Alignments

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
	(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:108
 aligned with RBM39_HUMAN | Q14498 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:113
                                   228       238       248       258       268       278       288       298       308       318       328   
          RBM39_HUMAN   219 LGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 331
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------2jrsA01 A:25-103  [code=3.30.70.330, no name defined]                          ----- CATH domains
               Pfam domains ---------------------------------RRM_1-2jrsA01 A:29-99                                                  --------- Pfam domains
         Sec.struct. author ..-----........................eeeeee......hhhhhhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh.........eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: - -------------------RRM  PDB: A:27-105 UniProt: 250-328                                            --- PROSITE
               Transcript 1 Exon 1.11c Exon 1.12b  PDB: A:7-52 UniProt: 230-275      Exon 1.13a            Exon 1.14a  PDB: A:75-108          Transcript 1
                 2jrs A   1 MG-----HHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
                             |     | 5        15        25        35        45        55        65        75        85        95       105   
                             2     3

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 2JRS)

CATH Domains (1, 1)

NMR Structure

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)

2jrsA01

A:25-103

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Homo sapiens (Human) (94)

RRM_1-2jrsA01

A:29-99

Gene Ontology (14, 14)

NMR Structure(hide GO term definitions)

Chain A (RBM39_HUMAN | Q14498)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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).
biological process
	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: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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	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.

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Related Entries

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UniProtKB/Swiss-Prot
	RBM39_HUMAN \| Q14498	:	2mhn 4oo6 4oz0 4oz1 4yud

Related Entries Specified in the PDB File

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