2JHT - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RHOGDI K135T,K138T,K141T MUTANT

Authors :   D. R. Cooper, K. Grelewska, Z. S. Derewenda

Date :   23 Feb 07 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

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)

Keywords :   Surface Entropy Reduction, Inhibitor, Gtpase Activation, Crystal Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Cooper, T. Boczek, K. Grelewska, M. Pinkowska, M. Sikorska, M. Zawadzki, Z. S. Derewenda
Protein Crystallization By Surface Entropy Reduction: Optimization Of The Ser Strategy
Acta Crystallogr. , Sect. D V. 63 636 2007
PubMed-ID: 17452789 | Reference-DOI: 10.1107/S0907444907010931

Molecule 1 - RHO GDP-DISSOCIATION INHIBITOR 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PGST-PARALLEL1
	Fragment	:	ISOPRENYL-BINDING DOMAIN, RESIDUES 66-201
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RHO GDI 1, RHO-GDI ALPHA

		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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	LI	1	Ligand/Ion	LITHIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	LI	-1	Ligand/Ion	LITHIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	LI	-1	Ligand/Ion	LITHIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	LI	-1	Ligand/Ion	LITHIUM ION
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	LI	-1	Ligand/Ion	LITHIUM ION
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:199 , LYS A:200 , ASP A:201 , HOH A:2100	BINDING SITE FOR RESIDUE SO4 A1203
2	AC2	SOFTWARE	SER D:148	BINDING SITE FOR RESIDUE LI A1204
3	AC3	SOFTWARE	MET A:145 , ARG B:152 , ALA B:153 , GLU B:154 , HOH B:2054 , HOH B:2055 , HOH B:2056 , HOH B:2057	BINDING SITE FOR RESIDUE SO4 B1203

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

Asymmetric Unit

No.	Residues
1	Val B:137	-	Thr B:138
2	Arg D:134	-	Thr D:135

(no "SAP(SNP)/Variant" information available for 2JHT)

(no "PROSITE Motif" information available for 2JHT)

Asymmetric Unit (4, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000269321	1a	ENSE00001297309	chr17:79829238-79829174	65	GDIR1_HUMAN	-	0	0	-	-
1.2	ENST00000269321	2	ENSE00000949422	chr17:79827833-79827617	217	GDIR1_HUMAN	1-64	64	0	-	-
1.3	ENST00000269321	3	ENSE00001293194	chr17:79827501-79827418	84	GDIR1_HUMAN	64-92	29	4	A:65-92 B:65-92 C:65-92 D:65-92	28 28 28 28
1.4	ENST00000269321	4	ENSE00001745599	chr17:79827282-79827206	77	GDIR1_HUMAN	92-117	26	4	A:92-117 B:92-117 C:92-117 D:92-117	26 26 26 26
1.5	ENST00000269321	5	ENSE00001617149	chr17:79827112-79827049	64	GDIR1_HUMAN	118-139	22	4	A:118-139 B:118-139 C:118-139 D:118-139	22 22 22 22
1.6b	ENST00000269321	6b	ENSE00001370626	chr17:79826951-79825598	1354	GDIR1_HUMAN	139-204	66	4	A:139-202 B:139-202 C:139-202 D:139-202	64 64 64 64

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:138
 aligned with GDIR1_HUMAN | P52565 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:138
                                    74        84        94       104       114       124       134       144       154       164       174       184       194        
          GDIR1_HUMAN    65 PNVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
               SCOP domains d2jhta_ A: automated matches                                                                                                               SCOP domains
               CATH domains 2jhtA00 A:65-202 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeee........eee....hhhhhhh.eeee...eeeeeeeeee....eeeeeeeeeeee...eeeeeeeeeeee..eeeeeeee...ee...hhhhheeeeeeeeee.......eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:65-92      -------------------------Exon 1.5              --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.4  PDB: A:92-117   ---------------------Exon 1.6b  PDB: A:139-202 UniProt: 139-204 [INCOMPLETE]          Transcript 1 (2)
                 2jht A  65 AMVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRTGVTIDTTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
                                    74        84        94       104       114       124       134       144       154       164       174       184       194

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with GDIR1_HUMAN | P52565 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:138
                                    74        84        94       104       114       124       134       144       154       164       174       184       194        
          GDIR1_HUMAN    65 PNVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
               SCOP domains d2jhtb_ B: automated matches                                                                                                               SCOP domains
               CATH domains 2jhtB00 B:65-202 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeee........eee......hhhhh.eeee...eeeeeeeeee....eeeeeeeeeee.....eeeeeeeeeee......eeee...ee........eeeeeeeeee.......eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:65-92      -------------------------Exon 1.5              --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.4  PDB: B:92-117   ---------------------Exon 1.6b  PDB: B:139-202 UniProt: 139-204 [INCOMPLETE]          Transcript 1 (2)
                 2jht B  65 AMVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRTGVTIDTTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
                                    74        84        94       104       114       124       134       144       154       164       174       184       194

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with GDIR1_HUMAN | P52565 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:138
                                    74        84        94       104       114       124       134       144       154       164       174       184       194        
          GDIR1_HUMAN    65 PNVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
               SCOP domains d2jhtc_ C: automated matches                                                                                                               SCOP domains
               CATH domains 2jhtC00 C:65-202 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeee........eee....hhhhhhh.eeee...eeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeee......eeee...ee........eeeeeeeeee.......eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: C:65-92      -------------------------Exon 1.5              --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.4  PDB: C:92-117   ---------------------Exon 1.6b  PDB: C:139-202 UniProt: 139-204 [INCOMPLETE]          Transcript 1 (2)
                 2jht C  65 AMVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRTGVTIDTTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
                                    74        84        94       104       114       124       134       144       154       164       174       184       194

Chain D from PDB  Type:PROTEIN  Length:138
 aligned with GDIR1_HUMAN | P52565 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:138
                                    74        84        94       104       114       124       134       144       154       164       174       184       194        
          GDIR1_HUMAN    65 PNVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
               SCOP domains d2jhtd_ D: automated matches                                                                                                               SCOP domains
               CATH domains 2jhtD00 D:65-202 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
           Pfam domains (1) --Rho_GDI-2jhtD01 D:67-201                                                                                                               - Pfam domains (1)
           Pfam domains (2) --Rho_GDI-2jhtD02 D:67-201                                                                                                               - Pfam domains (2)
           Pfam domains (3) --Rho_GDI-2jhtD03 D:67-201                                                                                                               - Pfam domains (3)
           Pfam domains (4) --Rho_GDI-2jhtD04 D:67-201                                                                                                               - Pfam domains (4)
         Sec.struct. author .....eeeeeeeee........eee...hhhhhh...eeee...eeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeee......eeee...ee........eeeeeeeeee.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: D:65-92      -------------------------Exon 1.5              --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.4  PDB: D:92-117   ---------------------Exon 1.6b  PDB: D:139-202 UniProt: 139-204 [INCOMPLETE]          Transcript 1 (2)
                 2jht D  65 AMVPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRTGVTIDTTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDW 202
                                    74        84        94       104       114       124       134       144       154       164       174       184       194

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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: E set domains (509)

Family: RhoGDI-like (34)

Protein domain: automated matches (8)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d2jhta_	A:
1b	d2jhtb_	B:
1c	d2jhtc_	C:
1d	d2jhtd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Coagulation Factor XIII; Chain A, domain 1 (28)

Homologous Superfamily: Coagulation Factor XIII, subunit A, domain 1 (22)

Human (Homo sapiens) (20)

1a	2jhtA00	A:65-202
1b	2jhtB00	B:65-202
1c	2jhtC00	C:65-202
1d	2jhtD00	D:65-202

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Rho_GDI] (12)

Family: Rho_GDI (12)

Homo sapiens (Human) (12)

1a	Rho_GDI-2jhtD01	D:67-201
1b	Rho_GDI-2jhtD02	D:67-201
1c	Rho_GDI-2jhtD03	D:67-201
1d	Rho_GDI-2jhtD04	D:67-201

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GDIR1_HUMAN | P52565)

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:0005094	Rho GDP-dissociation inhibitor activity	Prevents the dissociation of GDP from the small GTPase Rho, thereby preventing GTP from binding.
	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:0006928	movement of cell or subcellular component	The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0050771	negative regulation of axonogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
	GO:0007162	negative regulation of cell adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0050772	positive regulation of axonogenesis	Any process that activates or increases the frequency, rate or extent of axonogenesis.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
	GO:2000249	regulation of actin cytoskeleton reorganization	Any process that modulates the frequency, rate or extent of actin cytoskeleton reorganization.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	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:0071526	semaphorin-plexin signaling pathway	A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg D:134 - Thr D:135	[ RasMol ]
		Val B:137 - Thr B:138	[ RasMol ]

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	2jht
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1cc0	CRYSTAL STRUCTURE OF THE RHOA.GDP-RHOGDI COMPLEX
1fso	CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI QUADRUPLE MUTANT
1fst	CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI TRIPLE MUTANT
1ft0	CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI K113A MUTANT
1ft3	CRYSTAL STRUCTURE OF TRUNCATED RHOGDI K141A MUTANT
1hh4	RAC1-RHOGDI COMPLEX INVOLVED IN NADPH OXIDASE ACTIVATION
1kmt	CRYSTAL STRUCTURE OF RHOGDI GLU(154,155) ALA MUTANT
1qvy	CRYSTAL STRUCTURE OF RHOGDI K(199,200)R DOUBLE MUTANT
1rho	STRUCTURE OF RHO GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR
2bxw	CRYSTAL STRUCTURE OF RHOGDI LYS(135,138, 141)TYR MUTANT
2jhs	CRYSTAL STRUCTURE OF RHOGDI K135H,K138H, K141H MUTANT
2jhu	CRYSTAL STRUCTURE OF RHOGDI E154A,E155A MUTANT
2jhv	CRYSTAL STRUCTURE OF RHOGDI E154A,E155A MUTANT
2jhw	CRYSTAL STRUCTURE OF RHOGDI E155A, E157A MUTANT
2jhx	CRYSTAL STRUCTURE OF RHOGDI E155H, E157H MUTANT
2jhy	CRYSTAL STRUCTURE OF RHOGDI E155H, E157H MUTANT
2jhz	CRYSTAL STRUCTURE OF RHOGDI E155S, E157S MUTANT
2ji0	CRYSTAL STRUCTURE OF RHOGDI K138Y, K141Y MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (4, 16)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (18, 18)

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