3BYI - 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)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN RHO GTPASE ACTIVATING PROTEIN 15 (ARHGAP15)

Authors :   L. Shrestha, J. Tickle, J. Elkins, N. Burgess-Brown, C. Johansson, E. Papagrigoriou, K. Kavanagh, A. C. W. Pike, E. Ugochukwu, J. Uppenbe Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, D. Doyle, Structur Genomics Consortium (Sgc)

Date :   16 Jan 08 (Deposition) - 26 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Rho Gtpase, Bm046, Arhgap15, Structural Genomics Consortium, Sgc, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Shrestha, J. Tickle, J. Elkins, N. Burgess-Brown, C. Johansson, E. Papagrigoriou, K. Kavanagh, A. C. W. Pike, E. Ugochukwu, J. Uppenberg, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, D. Doyle
Crystal Structure Of Human Rho Gtpase Activating Protein 15 (Arhgap15).
To Be Published
PubMed: search

Molecule 1 - RHO GTPASE ACTIVATING PROTEIN 15
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)(R3)(PRARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 262-473
	Gene	:	ARHGAP15
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RHO GTPASE ACTIVATING PROTEIN 15, ISOFORM CRA_D

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3BYI)

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG15_HUMAN	281-470	4	A:281-470 B:281-470 C:281-470 D:281-470

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG15_HUMAN	281-470	1	A:281-470 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG15_HUMAN	281-470	1	- B:281-470 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG15_HUMAN	281-470	1	- - C:281-470 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG15_HUMAN	281-470	1	- - - D:281-470

Biological Unit 5 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG15_HUMAN	281-470	4	A:281-470 B:281-470 C:281-470 D:281-470

Asymmetric Unit (6, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000295095	3	ENSE00001273264	chr2:143886883-143887035	153	RHG15_HUMAN	-	0	0	-	-
1.4	ENST00000295095	4	ENSE00000964232	chr2:143913046-143913224	179	RHG15_HUMAN	1-55	55	0	-	-
1.6	ENST00000295095	6	ENSE00001070352	chr2:143959703-143959771	69	RHG15_HUMAN	56-78	23	0	-	-
1.7	ENST00000295095	7	ENSE00001070355	chr2:143973953-143974014	62	RHG15_HUMAN	79-99	21	0	-	-
1.9	ENST00000295095	9	ENSE00001070353	chr2:143986150-143986237	88	RHG15_HUMAN	99-128	30	0	-	-
1.12	ENST00000295095	12	ENSE00001070354	chr2:144008080-144008169	90	RHG15_HUMAN	129-158	30	0	-	-
1.13	ENST00000295095	13	ENSE00000995615	chr2:144193170-144193268	99	RHG15_HUMAN	159-191	33	0	-	-
1.14	ENST00000295095	14	ENSE00000995614	chr2:144194482-144194611	130	RHG15_HUMAN	192-235	44	0	-	-
1.15	ENST00000295095	15	ENSE00001273292	chr2:144244942-144245064	123	RHG15_HUMAN	235-276	42	4	A:261-276 B:261-276 C:263-276 D:263-276	16 16 14 14
1.16	ENST00000295095	16	ENSE00001207847	chr2:144276835-144276933	99	RHG15_HUMAN	276-309	34	4	A:276-309 B:276-309 C:276-309 D:276-309	34 34 34 34
1.17	ENST00000295095	17	ENSE00001207841	chr2:144313977-144314054	78	RHG15_HUMAN	309-335	27	4	A:309-335 B:309-335 C:309-335 D:309-335	27 27 27 27
1.22	ENST00000295095	22	ENSE00001751267	chr2:144381702-144381836	135	RHG15_HUMAN	335-380	46	4	A:335-380 B:335-380 C:335-380 D:335-380	46 46 46 46
1.23	ENST00000295095	23	ENSE00001070361	chr2:144460988-144461093	106	RHG15_HUMAN	380-415	36	4	A:380-415 B:380-415 C:380-415 D:380-415	36 36 36 36
1.24	ENST00000295095	24	ENSE00001273181	chr2:144525558-144525921	364	RHG15_HUMAN	415-475	61	4	A:415-471 B:415-471 C:415-472 D:415-471	57 57 58 57

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:211
 aligned with RHG15_HUMAN | Q53QZ3 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:211
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470 
          RHG15_HUMAN   261 RRPSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFG 471
               SCOP domains d3byia_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 3byiA00 A:261-471 GTPase -GAP domain                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------RHOGAP  PDB: A:281-470 UniProt: 281-470                                                                                                                                                       - PROSITE
           Transcript 1 (1) Exon 1.15       --------------------------------Exon 1.17  PDB: A:309-335  --------------------------------------------Exon 1.23  PDB: A:380-415           -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.16  PDB: A:276-309         -------------------------Exon 1.22  PDB: A:335-380 UniProt: 335-380    ----------------------------------Exon 1.24  PDB: A:415-471 UniProt: 415-475 [INCOMPLETE]   Transcript 1 (2)
                 3byi A 261 MRPSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFG 471
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with RHG15_HUMAN | Q53QZ3 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:211
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470 
          RHG15_HUMAN   261 RRPSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFG 471
               SCOP domains d3byib_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 3byiB00 B:261-471 GTPase -GAP domain                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..........hhhhhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------RHOGAP  PDB: B:281-470 UniProt: 281-470                                                                                                                                                       - PROSITE
           Transcript 1 (1) Exon 1.15       --------------------------------Exon 1.17  PDB: B:309-335  --------------------------------------------Exon 1.23  PDB: B:380-415           -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.16  PDB: B:276-309         -------------------------Exon 1.22  PDB: B:335-380 UniProt: 335-380    ----------------------------------Exon 1.24  PDB: B:415-471 UniProt: 415-475 [INCOMPLETE]   Transcript 1 (2)
                 3byi B 261 MRPSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFG 471
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with RHG15_HUMAN | Q53QZ3 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:210
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472
          RHG15_HUMAN   263 PSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFGS 472
               SCOP domains d3byic_ C: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 3byiC00 C:263-472 GTPase -GAP domain                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..........hhhhhhhhh....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------RHOGAP  PDB: C:281-470 UniProt: 281-470                                                                                                                                                       -- PROSITE
           Transcript 1 (1) Exon 1.15     --------------------------------Exon 1.17  PDB: C:309-335  --------------------------------------------Exon 1.23  PDB: C:380-415           --------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.16  PDB: C:276-309         -------------------------Exon 1.22  PDB: C:335-380 UniProt: 335-380    ----------------------------------Exon 1.24  PDB: C:415-472 UniProt: 415-475 [INCOMPLETE]    Transcript 1 (2)
                 3byi C 263 PSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFGS 472
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472

Chain D from PDB  Type:PROTEIN  Length:209
 aligned with RHG15_HUMAN | Q53QZ3 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:209
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462         
          RHG15_HUMAN   263 PSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFG 471
               SCOP domains d3byid_ D: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 3byiD00 D:263-471 GTPase -GAP domain                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------RHOGAP  PDB: D:281-470 UniProt: 281-470                                                                                                                                                       - PROSITE
           Transcript 1 (1) Exon 1.15     --------------------------------Exon 1.17  PDB: D:309-335  --------------------------------------------Exon 1.23  PDB: D:380-415           -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.16  PDB: D:276-309         -------------------------Exon 1.22  PDB: D:335-380 UniProt: 335-380    ----------------------------------Exon 1.24  PDB: D:415-471 UniProt: 415-475 [INCOMPLETE]   Transcript 1 (2)
                 3byi D 263 PSLKTLQEKGLIKDQIFGSHLHKVCERENSTVPWFVKQCIEAVEKRGLDVDGIYRVSGNLATIQKLRFIVNQEEKLNLDDSQWEDIHVVTGALKMFFRELPEPLFPYSFFEQFVEAIKKQDNNTRIEAVKSLVQKLPPPNRDTMKVLFGHLTKIVAKASKNLMSTQSLGIVFGPTLLRAENETGNMAIHMVYQNQIAELMLSEYSKIFG 471
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: GTPase activation domain, GAP (18)

Superfamily: GTPase activation domain, GAP (18)

Family: automated matches (6)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d3byia_	A:
1b	d3byib_	B:
1c	d3byic_	C:
1d	d3byid_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Phosphatidylinositol 3-kinase; Chain A (12)

Homologous Superfamily: GTPase -GAP domain (12)

Human (Homo sapiens) (10)

1a	3byiD00	D:263-471
1b	3byiC00	C:263-472
1c	3byiA00	A:261-471
1d	3byiB00	B:261-471

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RHG15_HUMAN | Q53QZ3)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
biological process
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0051056	regulation of small GTPase mediated signal transduction	Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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