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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE SECOND SH3 DOMAIN OF HUMAN RIM-BINDING PROTEIN 2

Authors :   K. Inoue, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   22 May 05 (Deposition) - 22 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Sh3 Domain, Rim Binding Protein 2, Rim-Bp2, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Inoue, F. Hayashi, S. Yokoyama
Solution Structure Of The Second Sh3 Domain Of Human Rim-Binding Protein 2
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RIM BINDING PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040705-05
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3 DOMAIN
	Gene	:	KAZUSA CDNA HG00364
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	RIM-BP2


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2CSQ)

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

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057715	D	888	N	RIMB2_HUMAN	Polymorphism	11060869	A	D	55	N

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

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	RIMB2_HUMAN	167-234 848-916 952-1019	2	- A:15-83 A:94-97

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000261655	1	ENSE00001225399	chr12:131002410-131002373	38	RIMB2_HUMAN	-	0	0	-	-
1.2	ENST00000261655	2	ENSE00001121163	chr12:130991315-130991193	123	RIMB2_HUMAN	-	0	0	-	-
1.3	ENST00000261655	3	ENSE00002176189	chr12:130963561-130963457	105	RIMB2_HUMAN	1-34	34	0	-	-
1.4	ENST00000261655	4	ENSE00001656454	chr12:130941245-130941041	205	RIMB2_HUMAN	35-103	69	0	-	-
1.5	ENST00000261655	5	ENSE00000757527	chr12:130935885-130935740	146	RIMB2_HUMAN	103-151	49	0	-	-
1.6	ENST00000261655	6	ENSE00000938260	chr12:130934821-130934745	77	RIMB2_HUMAN	152-177	26	0	-	-
1.7	ENST00000261655	7	ENSE00000938261	chr12:130929814-130929705	110	RIMB2_HUMAN	177-214	38	0	-	-
1.8	ENST00000261655	8	ENSE00000757523	chr12:130927205-130926393	813	RIMB2_HUMAN	214-485	272	0	-	-
1.9	ENST00000261655	9	ENSE00000757521	chr12:130923061-130922910	152	RIMB2_HUMAN	485-535	51	0	-	-
1.10	ENST00000261655	10	ENSE00000757520	chr12:130921836-130921387	450	RIMB2_HUMAN	536-685	150	0	-	-
1.11	ENST00000261655	11	ENSE00000757519	chr12:130919425-130919279	147	RIMB2_HUMAN	686-734	49	0	-	-
1.13	ENST00000261655	13	ENSE00000757518	chr12:130912882-130912724	159	RIMB2_HUMAN	735-787	53	0	-	-
1.14	ENST00000261655	14	ENSE00000757517	chr12:130907106-130906998	109	RIMB2_HUMAN	788-824	37	1	A:1-5	5
1.15	ENST00000261655	15	ENSE00000757516	chr12:130898851-130898670	182	RIMB2_HUMAN	824-884	61	1	A:6-51	46
1.16	ENST00000261655	16	ENSE00000903693	chr12:130897332-130897164	169	RIMB2_HUMAN	885-941	57	1	A:52-91	40
1.17	ENST00000261655	17	ENSE00000903691	chr12:130892374-130892271	104	RIMB2_HUMAN	941-975	35	1	A:92-96 (gaps)	24
1.18	ENST00000261655	18	ENSE00000757511	chr12:130890788-130890717	72	RIMB2_HUMAN	976-999	24	0	-	-
1.19	ENST00000261655	19	ENSE00000903689	chr12:130884358-130884224	135	RIMB2_HUMAN	1000-1044	45	0	-	-
1.20	ENST00000261655	20	ENSE00001425478	chr12:130883706-130880682	3025	RIMB2_HUMAN	1045-1052	8	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:97
 aligned with RIMB2_HUMAN | O15034 from UniProtKB/Swiss-Prot  Length:1052

    Alignment length:176
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977      
          RIMB2_HUMAN   808 GSAGPQRSRPVTVPSIDDYGRDRLSPDFYEESETDPGAEELPARIFVALFDYDPLTMSPNPDAAEEELPFKEGQIIKVYGDKDADGFYRGETCARLGLIPCNMVSEIQADDEEMMDQLLRQGFLPLNTPVEKIERSRRSGRRHSVSTRRMVALYDYDPRESSPNVDVEAELTFCTG 983
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------2csqA01 A:17-81 SH3 Domains                                      --------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--------------------------............eeee............hhhhhh.........eeeeeeee....eeeeee..eeeeee....ee...........---------------------..-----------------.--..-------------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------N----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SH3  PDB: A:15-83 UniProt: 848-916                                   -----------------------------------SH3  PDB: A:94-97                PROSITE
           Transcript 1 (1) Exon 1.14        ------------------------------------------------------------Exon 1.16  PDB: A:52-91 UniProt: 885-941 [INCOMPLETE]    ----------------------------------1.18     Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.15  PDB: A:6-51 UniProt: 824-884 [INCOMPLETE]         --------------------------------------------------------Exon 1.17  PDB: A:92-96 (gaps)     -------- Transcript 1 (2)
                 2csq A   1 GSSGS--------------------------SGTDPGAEELPARIFVALFDYDPLTMSPNPDAAEEELPFKEGQIIKVYGDKDADGFYRGETCARLGLIPCNMVSEIQADDEEMMDQ---------------------SG-----------------P--SS-------------G  97
                                |    -         -         - |      14        24        34        44        54        64        74        84      |  -         -        93         -       | -||       -     |
                                5                          6                                                                                   91                    92|                94 95|            97
                                                                                                                                                                      93                    96

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	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 2CSQ)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Human (Homo sapiens) (133)

2csqA01

A:17-81

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

NMR Structure(hide GO term definitions)

Chain A (RIMB2_HUMAN | O15034)

biological process
	GO:0010923	negative regulation of phosphatase activity	Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

NMR Structure
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