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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RHOGEF PROTEIN ASEF

Authors :   K. Murayama, M. Kato-Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   22 Aug 06 (Deposition) - 02 Jan 07 (Release) - 17 Jun 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

Chains :   Asym./Biol. Unit : A

Keywords :   Rho-Gef, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Murayama, M. Shirouzu, Y. Kawasaki, M. Kato-Murayama, K. Hanawa-Suetsugu, A. Sakamoto, Y. Katsura, A. Suenaga, M. Toyama, T. Terada, M. Taiji, T. Akiyama, S. Yokoyama
Crystal Structure Of The Rac Activator, Asef, Reveals Its Autoinhibitory Mechanism
J. Biol. Chem. V. 282 4238 2007
PubMed-ID: 17190834 | Reference-DOI: 10.1074/JBC.C600234200
(for further references see the PDB file header)

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE PROTEIN SYNTHESIS
	Expression System Plasmid	:	PX041202-06-MD01
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 59-540
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR, ASEF

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2DX1)

(no "SS Bond" information available for 2DX1)

(no "Cis Peptide Bond" information available for 2DX1)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035971	T	441	R	ARHG4_HUMAN	Unclassified	---	A	T	370	R
2	CancerSNP	VAR_ARHG4_HUMAN_CCDS2165_1_02 *	T	441	R	ARHG4_HUMAN	Disease (Breast cancer)	---	A	T	370	R
	* ID not provided by source

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

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	ARHG4_HUMAN	201-253	1	A:130-182
2	DH_2	PS50010	Dbl homology (DH) domain profile.	ARHG4_HUMAN	284-468	1	A:213-397
3	DH_1	PS00741	Dbl homology (DH) domain signature.	ARHG4_HUMAN	416-441	1	A:345-370
4	PH_DOMAIN	PS50003	PH domain profile.	ARHG4_HUMAN	499-606	1	A:428-535

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3c	ENST00000326016	3c	ENSE00001205109	chr2:131674224-131674634	411	ARHG4_HUMAN	-	0	0	-	-
1.3e	ENST00000326016	3e	ENSE00001287977	chr2:131674970-131675071	102	ARHG4_HUMAN	-	0	0	-	-
1.4a	ENST00000326016	4a	ENSE00001720558	chr2:131688525-131688830	306	ARHG4_HUMAN	1-100	100	0	-	-
1.5a	ENST00000326016	5a	ENSE00001173924	chr2:131704082-131704208	127	ARHG4_HUMAN	101-143	43	0	-	-
1.7	ENST00000326016	7	ENSE00001070783	chr2:131785518-131785657	140	ARHG4_HUMAN	143-189	47	1	A:114-118	5
1.10	ENST00000326016	10	ENSE00000921654	chr2:131796426-131796605	180	ARHG4_HUMAN	190-249	60	1	A:119-178	60
1.11c	ENST00000326016	11c	ENSE00000921655	chr2:131797589-131797765	177	ARHG4_HUMAN	250-308	59	1	A:179-237 (gaps)	59
1.12b	ENST00000326016	12b	ENSE00000921658	chr2:131797834-131798013	180	ARHG4_HUMAN	309-368	60	1	A:238-297	60
1.13b	ENST00000326016	13b	ENSE00000921660	chr2:131798803-131799035	233	ARHG4_HUMAN	369-446	78	1	A:298-375	78
1.13g	ENST00000326016	13g	ENSE00000921662	chr2:131799388-131799517	130	ARHG4_HUMAN	446-489	44	1	A:375-418	44
1.14a	ENST00000326016	14a	ENSE00000921663	chr2:131801025-131801156	132	ARHG4_HUMAN	490-533	44	1	A:419-462	44
1.15a	ENST00000326016	15a	ENSE00000921665	chr2:131801872-131802115	244	ARHG4_HUMAN	534-615	82	1	A:463-538 (gaps)	76
1.16a	ENST00000326016	16a	ENSE00000921668	chr2:131802942-131803019	78	ARHG4_HUMAN	615-641	27	0	-	-
1.16g	ENST00000326016	16g	ENSE00001821442	chr2:131803611-131804826	1216	ARHG4_HUMAN	641-690	50	0	-	-

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:385
 aligned with ARHG4_HUMAN | Q9NR80 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:425
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604     
          ARHG4_HUMAN   185 LAINELISDGSVVCAEALWDHVTMDDQELGFKAGDVIEVMDATNREWWWGRVADGEGWFPASFVRLRVNQDEPADDDAPLAGNSGAEDGGAEAQSSKDQMRTNVINEILSTERDYIKHLRDICEGYVRQCRKRADMFSEEQLRTIFGNIEDIYRCQKAFVKALEQRFNRERPHLSELGACFLEHQADFQIYSEYCNNHPNACVELSRLTKLSKYVYFFEACRLLQKMIDISLDGFLLTPVQKICKYPLQLAELLKYTHPQHRDFKDVEAALHAMKNVAQLINERKRRLENIDKIAQWQSSIEDWEGEDLLVRSSELIYSGELTRVTQPQAKSQQRMFFLFDHQLIYCKKDLLRRDVLYYKGRLDMDGLEVVDLEDGKDRDLHVSIKNAFRLHRGATGDSHLLCTRKPEQKQRWLKAFAREREQVQ 609
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..eeeee..................eeeeee.....eeeee....eeeee...eee.....---------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..eeeeeeeeee......eeeeeeeee..eeeeeee.......eeeeeeee....eee-------------.eeeee..------.eeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) ----------------SH3  PDB: A:130-182 UniProt: 201-253                 ------------------------------DH_2  PDB: A:213-397 UniProt: 284-468                                                                                                                                                    ------------------------------PH_DOMAIN  PDB: A:428-535 UniProt: 499-606                                                                  --- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DH_1  PDB: A:345-370      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) 1.7  Exon 1.10  PDB: A:119-178 UniProt: 190-249                  Exon 1.11c  PDB: A:179-237 (gaps) UniProt: 250-308         Exon 1.12b  PDB: A:238-297 UniProt: 309-368                 Exon 1.13b  PDB: A:298-375 UniProt: 369-446                                   -------------------------------------------Exon 1.14a  PDB: A:419-462 UniProt: 490-533 Exon 1.15a  PDB: A:463-538 (gaps) UniProt: 534-615 [INCOMPLETE]              Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13g  PDB: A:375-418 UniProt: 446-489 ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2dx1 A 114 LAINELISDGSVVCAEALWDHVTmDDQELGFKAGDVIEVmDATNREWWWGRVADGEGWFPASFVRLRVNQD---------------------AQSSKDQmRTNVINEILSTERDYIKHLRDICEGYVRQCRKRADmFSEEQLRTIFGNIEDIYRCQKAFVKALEQRFNRERPHLSELGACFLEHQADFQIYSEYCNNHPNACVELSRLTKLSKYVYFFEACRLLQKmIDISLDGFLLTPVQKICKYPLQLAELLKYTHPQHRDFKDVEAALHAmKNVAQLINERKRRLENIDKIAQWQSSIEDWEGEDLLVRSSELIYSGELTRVTQPQAKSQQRmFFLFDHQLIYCKKDLLRRDVLYYKGRLDmDGLEVV-------------IKNAFRLH------SHLLCTRKPEQKQRWLKAFAREREQVQ 538
                                   123       133   |   143       153       163       173       183|        -         -  |    213       223       233       243     | 253       263       273       283       293       303       313       323       333      |343       353       363       373       383   |   393       403       413       423       433       443     | 453       463       473    |  483|        -    |  503 |     513       523       533     
                                                 137-MSE         153-MSE                        184                   206      |                                 249-MSE                                                                                    340-MSE                                        387-MSE                                                       449-MSE                      478-MSE84           498    505    512                          
                                                                                                                             213-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 '\|'

(no "SCOP Domain" information available for 2DX1)

(no "CATH Domain" information available for 2DX1)

(no "Pfam Domain" information available for 2DX1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ARHG4_HUMAN | Q9NR80)

molecular function
	GO:0030676	Rac guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005089	Rho guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
biological process
	GO:0046847	filopodium assembly	The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
	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:0030032	lamellipodium assembly	Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein 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.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	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.
	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:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (2, 2)

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Exons (8, 8)

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