1QVY - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RHOGDI K(199,200)R DOUBLE MUTANT

Authors :   J. Czepas, Y. Devedjiev, D. Krowarsh, U. Derewenda, Z. S. Derewenda

Date :   29 Aug 03 (Deposition) - 10 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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 :   Protein Crystallization; Rational Surface Mutagenesis; Rhogdi; High Resolution; X-Ray Diffraction, Signaling Protein Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Czepas, Y. Devedjiev, D. Krowarsch, U. Derewenda, J. Otlewski, Z. S. Derewenda
The Impact Of Lys-->Arg Surface Mutations On The Crystallization Of The Globular Domain Of Rhogdi.
Acta Crystallogr. , Sect. D V. 60 275 2004
PubMed-ID: 14747703 | Reference-DOI: 10.1107/S0907444903026271
(for further references see the PDB file header)

Molecule 1 - RHO GDP-DISSOCIATION INHIBITOR 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGST-PARALLEL
	Expression System Strain	:	XL-10 GOLD, EPICURIAN COLI BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RHO GDI 1

		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 (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 2)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:199 , ARG A:200 , HOH A:1096 , HOH A:1140 , HOH A:1142 , HOH A:1148 , HOH A:1172 , ARG B:199	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	ARG A:199 , ARG B:172 , ARG B:199 , ARG B:200 , HOH B:1113 , HOH B:1158 , HOH B:1223	BINDING SITE FOR RESIDUE SO4 B 1002
3	AC3	SOFTWARE	ARG C:199 , ARG C:200 , HOH C:1063 , HOH C:1074 , HOH C:1080 , ARG D:199	BINDING SITE FOR RESIDUE SO4 C 1003
4	AC4	SOFTWARE	ARG C:199 , ARG D:172 , ARG D:199 , ARG D:200 , HOH D:1067 , HOH D:1115	BINDING SITE FOR RESIDUE SO4 D 1004
5	AC5	SOFTWARE	VAL A:78 , ARG A:111	BINDING SITE FOR RESIDUE SO4 A 1005
6	AC6	SOFTWARE	PRO A:68 , ASN A:69 , ARG A:120	BINDING SITE FOR RESIDUE SO4 A 1006
7	AC7	SOFTWARE	HIS B:131 , ARG B:180 , HOH B:1145 , HOH B:1181 , HOH B:1210	BINDING SITE FOR RESIDUE SO4 B 1007
8	AC8	SOFTWARE	HIS D:131 , ARG D:180 , HOH D:1056 , HOH D:1076 , HOH D:1200 , HOH D:1201	BINDING SITE FOR RESIDUE SO4 D 1008

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

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

(no "SAP(SNP)/Variant" information available for 1QVY)

(no "PROSITE Motif" information available for 1QVY)

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:67-92 B:67-92 C:67-92 D:67-92	26 26 26 26
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:139-204 B:139-204 C:139-204 D:139-204	66 66 66 66

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

    Alignment length:138
                                    76        86        96       106       116       126       136       146       156       166       176       186       196        
          GDIR1_HUMAN    67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDWKD 204
               SCOP domains d1qvya_ A: Rho GDP-dissociation inhibitor 1, RhoGDI                                                                                        SCOP domains
               CATH domains 1qvyA00 A:67-204 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee........eee...hhhhhhhh.eeee...eeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeee......eeee...ee...hhhhheeeeeeeeee.......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:67-92    -------------------------Exon 1.5              ----------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4  PDB: A:92-117   ---------------------Exon 1.6b  PDB: A:139-204 UniProt: 139-204                         Transcript 1 (2)
                 1qvy A  67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIRRDWKD 204
                                    76        86        96       106       116       126       136       146       156       166       176       186       196

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

    Alignment length:138
                                    76        86        96       106       116       126       136       146       156       166       176       186       196        
          GDIR1_HUMAN    67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDWKD 204
               SCOP domains d1qvyb_ B: Rho GDP-dissociation inhibitor 1, RhoGDI                                                                                        SCOP domains
               CATH domains 1qvyB00 B:67-204 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee........eee...hhhhhhhh.eeee...eeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeee......eeee...ee...hhhhheeeeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:67-92    -------------------------Exon 1.5              ----------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4  PDB: B:92-117   ---------------------Exon 1.6b  PDB: B:139-204 UniProt: 139-204                         Transcript 1 (2)
                 1qvy B  67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIRRDWKD 204
                                    76        86        96       106       116       126       136       146       156       166       176       186       196

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

    Alignment length:138
                                    76        86        96       106       116       126       136       146       156       166       176       186       196        
          GDIR1_HUMAN    67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDWKD 204
               SCOP domains d1qvyc_ C: Rho GDP-dissociation inhibitor 1, RhoGDI                                                                                        SCOP domains
               CATH domains 1qvyC00 C:67-204 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee........eee...hhhhhh...eeee...eeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeee......eeee...ee...hhhhheeeeeeeeee.......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: C:67-92    -------------------------Exon 1.5              ----------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4  PDB: C:92-117   ---------------------Exon 1.6b  PDB: C:139-204 UniProt: 139-204                         Transcript 1 (2)
                 1qvy C  67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIRRDWKD 204
                                    76        86        96       106       116       126       136       146       156       166       176       186       196

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

    Alignment length:138
                                    76        86        96       106       116       126       136       146       156       166       176       186       196        
          GDIR1_HUMAN    67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKDWKD 204
               SCOP domains d1qvyd_ D: Rho GDP-dissociation inhibitor 1, RhoGDI                                                                                        SCOP domains
               CATH domains 1qvyD00 D:67-204 Coagulation Factor XIII, subunit A, domain 1                                                                              CATH domains
           Pfam domains (1) Rho_GDI-1qvyD01 D:67-201                                                                                                               --- Pfam domains (1)
           Pfam domains (2) Rho_GDI-1qvyD02 D:67-201                                                                                                               --- Pfam domains (2)
           Pfam domains (3) Rho_GDI-1qvyD03 D:67-201                                                                                                               --- Pfam domains (3)
           Pfam domains (4) Rho_GDI-1qvyD04 D:67-201                                                                                                               --- Pfam domains (4)
         Sec.struct. author ...eeeeeeeee........eee...hhhhhhhh.eeee...eeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeee......eeee...ee...hhhhheeeeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: D:67-92    -------------------------Exon 1.5              ----------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4  PDB: D:92-117   ---------------------Exon 1.6b  PDB: D:139-204 UniProt: 139-204                         Transcript 1 (2)
                 1qvy D  67 VPNVVVTGLTLVCSSAPGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTYRKGVKIDKTDYMVGSYGPRAEEYEFLTPVEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIRRDWKD 204
                                    76        86        96       106       116       126       136       146       156       166       176       186       196

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: Rho GDP-dissociation inhibitor 1, RhoGDI (16)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d1qvya_	A:
1b	d1qvyb_	B:
1c	d1qvyc_	C:
1d	d1qvyd_	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	1qvyA00	A:67-204
1b	1qvyB00	B:67-204
1c	1qvyC00	C:67-204
1d	1qvyD00	D:67-204

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Rho_GDI (12)

Homo sapiens (Human) (12)

1a	Rho_GDI-1qvyD01	D:67-201
1b	Rho_GDI-1qvyD02	D:67-201
1c	Rho_GDI-1qvyD03	D:67-201
1d	Rho_GDI-1qvyD04	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.

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	1qvy
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1kmt	THE SAME PROTEIN E(154,155) DOUBLE MUTANT
1rho	THE SAME PROTEIN WILD TYPE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (4, 16)

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