2EK1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RNA-BINDING MOTIF OF HUMAN RNA-BINDING PROTEIN 12

Authors :   Ihsanawati, Y. Bessho, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   22 Mar 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Rna Recognition Motif, Dimer, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Ihsanawati, Y. Bessho, M. Shirouzu, S. Yokoyama
Crystal Structure Of Rna-Binding Motif Of Human Rna-Binding Protein 12
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RNA-BINDING PROTEIN 12
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System Plasmid	:	PX041122-21
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 861-955
	Gene	:	RBM12, KIAA0765
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE SYSTEM
	Synonym	:	RRM, RNA-BINDING MOTIF PROTEIN 12, SH3/WW DOMAIN ANCHOR PROTEIN IN THE NUCLEUS, SWAN

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 24)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2EK1)

Asymmetric Unit

No.	Residues
1	A:907	-	B:907
2	C:907	-	D:907
3	E:907	-	F:907
4	G:907	-	H:907

Asymmetric Unit

No.	Residues
1	Gly B:951	-	Pro B:952
2	Gly C:951	-	Pro C:952
3	Gly D:951	-	Pro D:952
4	Gly E:951	-	Pro E:952

Asymmetric Unit (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052218	P	921	L	RBM12_HUMAN	Polymorphism	6121012	A/B/C/D/E/F/G/H	P	941	L

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052218	P	921	L	RBM12_HUMAN	Polymorphism	6121012	A/B	P	941	L

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052218	P	921	L	RBM12_HUMAN	Polymorphism	6121012	C/D	P	941	L

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

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052218	P	921	L	RBM12_HUMAN	Polymorphism	6121012	E/F	P	941	L

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

Biological Unit 4 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052218	P	921	L	RBM12_HUMAN	Polymorphism	6121012	G/H	P	941	L

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

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM12_HUMAN	304-379 430-507 856-932	8	- - A:876-949 B:876-949 C:876-949 D:876-949 E:876-949 F:876-949 G:876-949 H:876-949

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM12_HUMAN	304-379 430-507 856-932	2	- - A:876-949 B:876-949 - - - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM12_HUMAN	304-379 430-507 856-932	2	- - - - C:876-949 D:876-949 - - - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM12_HUMAN	304-379 430-507 856-932	2	- - - - - - E:876-949 F:876-949 - -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM12_HUMAN	304-379 430-507 856-932	2	- - - - - - - - G:876-949 H:876-949

Asymmetric Unit (1, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000374114	1c	ENSE00002160337	chr20:34252838-34252682	157	RBM12_HUMAN	-	0	0	-	-
1.2a	ENST00000374114	2a	ENSE00002144940	chr20:34246936-34246852	85	RBM12_HUMAN	-	0	0	-	-
1.3f	ENST00000374114	3f	ENSE00001462525	chr20:34243266-34236847	6420	RBM12_HUMAN	1-940	940	8	A:875-952 B:875-952 C:875-952 D:874-952 E:875-952 F:875-952 G:876-952 H:875-952	78 78 78 79 78 78 77 78

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:79
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:79
                                                                                                       932 
                                   864       874       884       894       904       914       924       | 
          RBM12_HUMAN   855 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-   -
               SCOP domains d2ek1a_ A: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhh..........eeee.....eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------L------------ SAPs(SNPs)
                    PROSITE -RRM  PDB: A:876-949 UniProt: 856-932                                         - PROSITE
               Transcript 1 Exon 1.3f  PDB: A:875-952 UniProt: 1-940 [INCOMPLETE]                         - Transcript 1
                 2ek1 A 875 PTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS 953
                                   884       894       904       914|     |924       934       944         
                                  883-MSE                         915-MSE |                                
                                                                        921-MSE

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:78
                                   864       874       884       894       904       914       924        
          RBM12_HUMAN   855 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 932
               SCOP domains d2ek1b_ B: automated matches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhh..........eeee.....eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------L----------- SAPs(SNPs)
                    PROSITE -RRM  PDB: B:876-949 UniProt: 856-932                                          PROSITE
               Transcript 1 Exon 1.3f  PDB: B:875-952 UniProt: 1-940 [INCOMPLETE]                          Transcript 1
                 2ek1 B 875 PTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 952
                                   884       894       904       914|     |924       934       944        
                                  883-MSE                         915-MSE |                               
                                                                        921-MSE

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:79
                                                                                                       932 
                                   864       874       884       894       904       914       924       | 
          RBM12_HUMAN   855 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-   -
               SCOP domains d2ek1c_ C: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhh..........eeee.....eeeeeeeee.hhhhhhhhhhhhh.........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------L------------ SAPs(SNPs)
                    PROSITE -RRM  PDB: C:876-949 UniProt: 856-932                                         - PROSITE
               Transcript 1 Exon 1.3f  PDB: C:875-952 UniProt: 1-940 [INCOMPLETE]                         - Transcript 1
                 2ek1 C 875 PTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS 953
                                   884       894       904       914|     |924       934       944         
                                  883-MSE                         915-MSE |                                
                                                                        921-MSE

Chain D from PDB  Type:PROTEIN  Length:79
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:79
                                   863       873       883       893       903       913       923         
          RBM12_HUMAN   854 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 932
               SCOP domains d2ek1d_ D: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhh..........eeee.....eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------L----------- SAPs(SNPs)
                    PROSITE --RRM  PDB: D:876-949 UniProt: 856-932                                          PROSITE
               Transcript 1 Exon 1.3f  PDB: D:874-952 UniProt: 1-940 [INCOMPLETE]                           Transcript 1
                 2ek1 D 874 GPTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 952
                                   883       893       903       913 |     923       933       943         
                                   883-MSE                         915-MSE |                               
                                                                         921-MSE

Chain E from PDB  Type:PROTEIN  Length:79
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:79
                                                                                                       932 
                                   864       874       884       894       904       914       924       | 
          RBM12_HUMAN   855 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-   -
               SCOP domains d2ek1e_ E: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhh..........eeee.....eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------L------------ SAPs(SNPs)
                    PROSITE -RRM  PDB: E:876-949 UniProt: 856-932                                         - PROSITE
               Transcript 1 Exon 1.3f  PDB: E:875-952 UniProt: 1-940 [INCOMPLETE]                         - Transcript 1
                 2ek1 E 875 PTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS 953
                                   884       894       904       914|     |924       934       944         
                                  883-MSE                         915-MSE |                                
                                                                        921-MSE

Chain F from PDB  Type:PROTEIN  Length:79
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:79
                                                                                                       932 
                                   864       874       884       894       904       914       924       | 
          RBM12_HUMAN   855 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-   -
               SCOP domains d2ek1f_ F: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhh..........eeee.....eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------L------------ SAPs(SNPs)
                    PROSITE -RRM  PDB: F:876-949 UniProt: 856-932                                         - PROSITE
               Transcript 1 Exon 1.3f  PDB: F:875-952 UniProt: 1-940 [INCOMPLETE]                         - Transcript 1
                 2ek1 F 875 PTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS 953
                                   884       894       904       914|     |924       934       944         
                                  883-MSE                         915-MSE |                                
                                                                        921-MSE

Chain G from PDB  Type:PROTEIN  Length:77
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:77
                                   865       875       885       895       905       915       925       
          RBM12_HUMAN   856 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 932
               SCOP domains d2ek1g_ G: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhh..........eeee.....eeeeeeee..hhhhhhhhhhhhh.........eee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------L----------- SAPs(SNPs)
                    PROSITE RRM  PDB: G:876-949 UniProt: 856-932                                          PROSITE
               Transcript 1 Exon 1.3f  PDB: G:876-952 UniProt: 1-940 [INCOMPLETE]                         Transcript 1
                 2ek1 G 876 TVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 952
                                   885       895       905       915     | 925       935       945       
                                 883-MSE                         915-MSE |                               
                                                                       921-MSE

Chain H from PDB  Type:PROTEIN  Length:79
 aligned with RBM12_HUMAN | Q9NTZ6 from UniProtKB/Swiss-Prot  Length:932

    Alignment length:79
                                                                                                       932 
                                   864       874       884       894       904       914       924       | 
          RBM12_HUMAN   855 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-   -
               SCOP domains d2ek1h_ H: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhh..........eeee.....eeeeeeee..hhhhhhhhhhhhh..ee..ee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------L------------ SAPs(SNPs)
                    PROSITE -RRM  PDB: H:876-949 UniProt: 856-932                                         - PROSITE
               Transcript 1 Exon 1.3f  PDB: H:875-952 UniProt: 1-940 [INCOMPLETE]                         - Transcript 1
                 2ek1 H 875 PTVIKVQNmPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGmPTGEAmVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS 953
                                   884       894       904       914|     |924       934       944         
                                  883-MSE                         915-MSE |                                
                                                                        921-MSE

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 '\|'

Asymmetric Unit

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)

1a	d2ek1a_	A:
1b	d2ek1b_	B:
1c	d2ek1c_	C:
1d	d2ek1d_	D:
1e	d2ek1e_	E:
1f	d2ek1f_	F:
1g	d2ek1g_	G:
1h	d2ek1h_	H:

(no "CATH Domain" information available for 2EK1)

(no "Pfam Domain" information available for 2EK1)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (RBM12_HUMAN | Q9NTZ6)

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.
cellular component
	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.

Asymmetric Unit
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	Sites
(no "Sites" information available for 2ek1)

	Cis Peptide Bonds
		Gly B:951 - Pro B:952	[ RasMol ]
		Gly C:951 - Pro C:952	[ RasMol ]
		Gly D:951 - Pro D:952	[ RasMol ]
		Gly E:951 - Pro E:952	[ RasMol ]

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	2ek1
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	RBM12_HUMAN \| Q9NTZ6	:	1wel 2cpy 2dnn 2ek6

(no "Related Entries Specified in the PDB File" available for 2EK1)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 24)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 8)

PROSITE Motifs (1, 8)

Exons (1, 8)

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