3V53 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN RBM25

Authors :   D. S. Gong

Date :   16 Dec 11 (Deposition) - 12 Dec 12 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

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

Reference :   D. S. Gong, F. Yang, F. Li, D. Qian, M. Wu, Z. Shao, M. Wu, J. Wu, Y. Shi
Crystal Structure And Functional Characterization Of The Human Rbm25 Pwi Domain And Its Flanking Basic Region
Biochem. J. V. 450 85 2013
PubMed-ID: 23190262 | Reference-DOI: 10.1042/BJ20121382

Molecule 1 - RNA-BINDING PROTEIN 25
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 734-843
	Gene	:	RBM25
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ARG/GLU/ASP-RICH PROTEIN OF 120 KDA, RED120, PROTEIN S164, RNA-BINDING MOTIF PROTEIN 25, RNA-BINDING REGION-CONTAINING PROTEIN 7

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3V53)

(no "Site" information available for 3V53)

(no "SS Bond" information available for 3V53)

(no "Cis Peptide Bond" information available for 3V53)

(no "SAP(SNP)/Variant" information available for 3V53)

Asymmetric Unit (1, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWI	PS51025	PWI domain profile.	RBM25_HUMAN	750-843	5	A:750-841 B:750-841 C:750-839 D:750-839 E:750-838

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWI	PS51025	PWI domain profile.	RBM25_HUMAN	750-843	1	A:750-841 - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWI	PS51025	PWI domain profile.	RBM25_HUMAN	750-843	1	- B:750-841 - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWI	PS51025	PWI domain profile.	RBM25_HUMAN	750-843	1	- - C:750-839 - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWI	PS51025	PWI domain profile.	RBM25_HUMAN	750-843	1	- - - D:750-839 -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWI	PS51025	PWI domain profile.	RBM25_HUMAN	750-843	1	- - - - E:750-838

(no "Exon" information available for 3V53)

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:110
 aligned with RBM25_HUMAN | P49756 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:113
                                   738       748       758       768       778       788       798       808       818       828       838   
          RBM25_HUMAN   729 VNTEEKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGL 841
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------PWI  PDB: A:750-841 UniProt: 750-843                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3v53 A 729 HHHHMKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIG---ATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGL 841
                                   738       748       758       768       778     | 788       798       808       818       828       838   
                                                                                 784 788

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with RBM25_HUMAN | P49756 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:112
                                   739       749       759       769       779       789       799       809       819       829       839  
          RBM25_HUMAN   730 NTEEKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGL 841
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------PWI  PDB: B:750-841 UniProt: 750-843                                                         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3v53 B 730 HHHMKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKIGL 841
                                   739       749       759       769       779       789       799       809       819       829       839

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with RBM25_HUMAN | P49756 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:104
                                   745       755       765       775       785       795       805       815       825       835    
          RBM25_HUMAN   736 KHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKI 839
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PWI  PDB: C:750-839 UniProt: 750-843                                                       PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3v53 C 736 KHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKI 839
                                   745       755       765       775       785       795       805       815       825       835

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with RBM25_HUMAN | P49756 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:109
                                   740       750       760       770       780       790       800       810       820       830         
          RBM25_HUMAN   731 TEEKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKI 839
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PWI  PDB: D:750-839 UniProt: 750-843                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3v53 D 731 HHMKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKKI 839
                                   740       750       760       770       780       790       800       810       820       830

Chain E from PDB  Type:PROTEIN  Length:102
 aligned with RBM25_HUMAN | P49756 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:103
                                   745       755       765       775       785       795       805       815       825       835   
          RBM25_HUMAN   736 KHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKK 838
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhh........hhhhhhhhhhhhhhhhhhhhh-..hhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PWI  PDB: E:750-838 UniProt: 750-843                                                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3v53 E 736 KHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRIRPWINKKIIEYI-EEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLIYETEAKK 838
                                   745       755       765       775       785       795       805       815       825       835   
                                                                         783 |                                                     
                                                                           785

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 '\|'

(no "SCOP Domain" information available for 3V53)

(no "CATH Domain" information available for 3V53)

(no "Pfam Domain" information available for 3V53)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RBM25_HUMAN | P49756)

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).
biological process
	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:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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