2MHN - JenaLib

NMR Structure - model 1

NMR Structure - all models

collapse

expand

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   NMR STRUCTURE OF THE FIRST RRM DOMAIN OF THE PROTEIN RBM39 FROM HOMO SAPIENS

Authors :   P. Serrano, M. Geralt, S. K. Dutta, K. Wuthrich, Joint Center For Str Genomics (Jcsg), Partnership For T-Cell Biology (Tcell)

Date :   02 Dec 13 (Deposition) - 01 Jan 14 (Release) - 01 Jan 14 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   T-Cell, Psi-Biology, Rna Binding Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Serrano, K. Wuthrich, M. Geralt, S. K. Dutta
Nmr Structure Of The First Rrm Domain Of The Protein Rbm39 From Homo Sapiens
To Be Published
PubMed: search

Compounds

Molecule 1 - RNA-BINDING PROTEIN 39
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	469008
	Expression System Variant	:	DE3
	Expression System Vector	:	PSPEEDET
	Fragment	:	RRM 1 DOMAIN RESIDUES 144-234
	Gene	:	RBM39, HCC1, RNPC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HEPATOCELLULAR CARCINOMA PROTEIN 1, RNA-BINDING MOTIF PROTEIN 39, RNA-BINDING REGION-CONTAINING PROTEIN 2, SPLICING FACTOR HCC1

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2MHN)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

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:13-90

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:13-90

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	1	A:1-3	3
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	1	A:4-38	35
1.11c	ENST00000253363	11c	ENSE00002082263	chr20:34312644-34312492	153	RBM39_HUMAN	179-229	51	1	A:39-89	51
1.12b	ENST00000253363	12b	ENSE00001773401	chr20:34309799-34309662	138	RBM39_HUMAN	230-275	46	1	A:90-94	5
1.13a	ENST00000253363	13a	ENSE00001613700	chr20:34304727-34304662	66	RBM39_HUMAN	276-297	22	0	-	-
1.14a	ENST00000253363	14a	ENSE00001623326	chr20:34302311-34302107	205	RBM39_HUMAN	298-366	69	0	-	-
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:94
 aligned with RBM39_HUMAN | Q14498 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:125
                                   119       129       139       149       159       169       179       189       199       209       219       229     
          RBM39_HUMAN   110 GKIGLPHSIKLSRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNR 234
               SCOP domains d2m                               hna_ A: automated matches                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------------------------------..hhhhhhh.eeeee.......hhhhhhhhhh...eeee.............eeeeee...hhhhhhhh....hhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------RRM  PDB: A:13-90 UniProt: 153-230                                            ---- PROSITE
           Transcript 1 (1) Exon 1.8c   -----------------Exon 1.10c  PDB: A:4-38 UniProt: 139-178Exon 1.11c  PDB: A:39-89 UniProt: 179-229          1.12b Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.9a  PDB: -  ----------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2mhn A   1 GHM-------------------------------NLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNR  94
                              |      -         -         -    |    9        19        29        39        49        59        69        79        89     
                              3                               4

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 (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: automated matches (24)

Human (Homo sapiens) [TaxId: 9606] (21)

d2mhna_

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2MHN)

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.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2mhn)

	Sites
(no "Sites" information available for 2mhn)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mhn)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2mhn
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RBM39_HUMAN \| Q14498
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RBM39_HUMAN \| Q14498
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2MHN)