1XA6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN BETA2-CHIMAERIN

Authors :   B. Canagarajah, F. C. Leskow, J. Y. Ho, H. Mischak, L. F. Saidi, M. G. Kazanietz, J. H. Hurley

Date :   25 Aug 04 (Deposition) - 23 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A

Keywords :   Beta2-Chimaerin, Racgap, C1, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Canagarajah, F. C. Leskow, J. Y. Ho, H. Mischak, L. F. Saidi, M. G. Kazanietz, J. H. Hurley
Structural Mechanism For Lipid Activation Of The Rac-Specific Gap, Beta2-Chimaerin.
Cell(Cambridge, Mass. ) V. 119 407 2004
PubMed-ID: 15507211 | Reference-DOI: 10.1016/J.CELL.2004.10.012
(for further references see the PDB file header)

Molecule 1 - BETA2-CHIMAERIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector	:	PACG2T
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BETA-CHIMERIN, RHO-GTPASE-ACTIVATING PROTEIN 3

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:213 , CYS A:243 , CYS A:246 , CYS A:262	BINDING SITE FOR RESIDUE ZN A 467
2	AC2	SOFTWARE	CYS A:226 , CYS A:229 , HIS A:251 , CYS A:254	BINDING SITE FOR RESIDUE ZN A 468

(no "SS Bond" information available for 1XA6)

(no "Cis Peptide Bond" information available for 1XA6)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049136	P	438	S	CHIO_HUMAN	Polymorphism	34971642	A	P	436	S

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

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	CHIO_HUMAN	59-127	1	A:57-125
2	ZF_DAG_PE_2	PS50081	Zinc finger phorbol-ester/DAG-type profile.	CHIO_HUMAN	214-264	1	A:212-262
3	ZF_DAG_PE_1	PS00479	Zinc finger phorbol-ester/DAG-type signature.	CHIO_HUMAN	215-264	1	A:213-262
4	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	CHIO_HUMAN	277-468	1	A:275-466

Asymmetric/Biological Unit (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000222792	4a	ENSE00001389830	chr7:29234028-29234606	579	CHIO_HUMAN	1-17	17	0	-	-
1.13b	ENST00000222792	13b	ENSE00001701043	chr7:29394241-29394279	39	CHIO_HUMAN	17-30	14	1	A:21-28	8
1.14b	ENST00000222792	14b	ENSE00001716497	chr7:29407548-29407603	56	CHIO_HUMAN	30-48	19	1	A:28-46	19
1.17b	ENST00000222792	17b	ENSE00001632805	chr7:29433295-29433326	32	CHIO_HUMAN	49-59	11	1	A:47-57	11
1.18c	ENST00000222792	18c	ENSE00001730004	chr7:29437989-29438102	114	CHIO_HUMAN	59-97	39	1	A:57-95	39
1.20h	ENST00000222792	20h	ENSE00000674672	chr7:29440159-29440444	286	CHIO_HUMAN	97-192	96	1	A:95-161	67
1.21g	ENST00000222792	21g	ENSE00000674673	chr7:29519895-29519972	78	CHIO_HUMAN	193-218	26	1	A:209-216	8
1.23	ENST00000222792	23	ENSE00001652432	chr7:29535568-29535652	85	CHIO_HUMAN	219-247	29	1	A:217-245	29
1.24	ENST00000222792	24	ENSE00001675410	chr7:29539483-29539656	174	CHIO_HUMAN	247-305	59	1	A:245-303	59
1.25b	ENST00000222792	25b	ENSE00001614298	chr7:29544360-29544437	78	CHIO_HUMAN	305-331	27	1	A:303-329	27
1.26c	ENST00000222792	26c	ENSE00000674678	chr7:29546844-29546981	138	CHIO_HUMAN	331-377	47	1	A:329-375	47
1.27a	ENST00000222792	27a	ENSE00000674679	chr7:29548917-29549022	106	CHIO_HUMAN	377-412	36	1	A:375-410	36
1.28d	ENST00000222792	28d	ENSE00001581228	chr7:29552180-29553944	1765	CHIO_HUMAN	412-468	57	1	A:410-466	57

Asymmetric/Biological 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:399
 aligned with CHIO_HUMAN | P52757 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:446
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462      
           CHIO_HUMAN    23 PPIWKSYLYQLQQEAPRPKRIICPREVENRPKYYGREFHGIISREQADELLGGVEGAYILRESQRQPGCYTLALRFGNQTLNYRLFHDGKHFVGEKRFESIHDLVTDGLITLYIETKAAEYISKMTTNPIYEHIGYATLLREKVSRRLSRSKNEPRKTNVTHEEHTAVEKISSLVRRAALTHNDNHFNYEKTHNFKVHTFRGPHWCEYCANFMWGLIAQGVRCSDCGLNVHKQCSKHVPNDCQPDLKRIKKVYCCDLTTLVKAHNTQRPMVVDICIREIEARGLKSEGLYRVSGFTEHIEDVKMAFDRDGEKADISANVYPDINIITGALKLYFRDLPIPVITYDTYSKFIDAAKISNADERLEAVHEVLMLLPPAHYETLRYLMIHLKKVTMNEKDNFMNAENLGIVFGPTLMRPPEDSTLTTLHDMRYQKLIVQILIENEDVLF 468
               SCOP domains d1xa6a2 A:21-161 Beta-chimaerin, N-terminal domain                                                                                           -----------------------------------------------d1xa6a3 A:209-270 Beta-chimaerin, middle domain               d1xa6a1 A:271-466 Beta-chimaerin, C-terminal domain                                                                                                                                                  SCOP domains
               CATH domains --------------1xa6A01 A:35-138 SHC Adaptor Protein                                                                    ----------------------1                                               xa6A02 A:161-276  [code=3.30.60.20, no name defined]                1xa6A03 A:277-466 GTPase -GAP domain                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------SH2-1xa6A03 A:57-127                                                   -------------------------------------------------------------------------------------C1_1-1xa6A01 A:213-265                               -----------------------RhoGAP-1xa6A02 A:289-443                                                                                                                                   ----------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh......................eeee.hhhhhhhhhh.....eeeee.......eeeeeee..eeee...ee...ee.........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.......-----------------------------------------------........ee.....................ee..........hhhhh...................hhhhhhhhhh...hhhhhhhhhhhhhh............hhhhhhhhhhhhh...............hhhhhhhhhhhhhhh........hhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhh.......hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------------SH2  PDB: A:57-125 UniProt: 59-127                                   --------------------------------------------------------------------------------------ZF_DAG_PE_2  PDB: A:212-262 UniProt: 214-264       ------------RHOGAP  PDB: A:275-466 UniProt: 277-468                                                                                                                                                          PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_DAG_PE_1  PDB: A:213-262 UniProt: 215-264      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) 1.13b   ------------------Exon 1.17b -------------------------------------Exon 1.20h  PDB: A:95-161 UniProt: 97-192 [INCOMPLETE]                                          Exon 1.21g  PDB: A:209-216Exon 1.23  PDB: A:217-245    ---------------------------------------------------------Exon 1.25b  PDB: A:303-329 ---------------------------------------------Exon 1.27a  PDB: A:375-410          -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.14b         ----------Exon 1.18c  PDB: A:57-95 UniProt: 59-97-----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.24  PDB: A:245-303 UniProt: 247-305                 -------------------------Exon 1.26c  PDB: A:329-375 UniProt: 331-377    ----------------------------------Exon 1.28d  PDB: A:410-466 UniProt: 412-468               Transcript 1 (2)
                 1xa6 A  21 PPIWKSYLYQLQQEAPRPKRIICPREVENRPKYYGREFHGIISREQADELLGGVEGAYILRESQRQPGCYTLALRFGNQTLNYRLFHDGKHFVGEKRFESIHDLVTDGLITLYIETKAAEYISKMTTNPIYEHIGYATLLR-----------------------------------------------YEKTHNFKVHTFRGPHWCEYCANFMWGLIAQGVRCSDCGLNVHKQCSKHVPNDCQPDLKRIKKVYCCDLTTLVKAHNTQRPMVVDICIREIEARGLKSEGLYRVSGFTEHIEDVKMAFDRDGEKADISANVYPDINIITGALKLYFRDLPIPVITYDTYSKFIDAAKISNADERLEAVHEVLMLLPPAHYETLRYLMIHLKKVTMNEKDNFMNAENLGIVFGPTLMRPPEDSTLTTLHDMRYQKLIVQILIENEDVLF 466
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160|        -         -         -         -       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460      
                                                                                                                                                                      161                                             209

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SHC Adaptor Protein (206)

Homologous Superfamily: SHC Adaptor Protein (206)

Human (Homo sapiens) (147)

1xa6A01

A:35-138

Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1 (140)

Homologous Superfamily: [code=3.30.60.20, no name defined] (15)

Human (Homo sapiens) (5)

1xa6A02

A:161-276

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)

1xa6A03

A:277-466

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C1 (13)

Family: C1_1 (10)

Homo sapiens (Human) (4)

C1_1-1xa6A01

A:213-265

Clan: GAP (15)

Family: RhoGAP (12)

Homo sapiens (Human) (12)

RhoGAP-1xa6A02

A:289-443

Clan: no clan defined [family: SH2] (119)

Family: SH2 (119)

Homo sapiens (Human) (79)

SH2-1xa6A03

A:57-127

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CHIO_HUMAN | P52757)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	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.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (12, 12)

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