3RAN - 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 :   CANINE GDP-RAN Q69L MUTANT

Authors :   M. Stewart, H. M. Kent, A. J. Mccoy

Date :   19 Oct 98 (Deposition) - 02 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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 :   Gtpase, Nuclear Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Stewart, H. M. Kent, A. J. Mccoy
The Structure Of The Q69L Mutant Of Gdp-Ran Shows A Major Conformational Change In The Switch Ii Loop That Accounts For Its Failure To Bind Nuclear Transport Factor 2 (Ntf2).
J. Mol. Biol. V. 284 1517 1998
PubMed-ID: 9878368 | Reference-DOI: 10.1006/JMBI.1998.2204
(for further references see the PDB file header)

Molecule 1 - PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Other Details	:	Q69L MUTANT CONSTRUCTED BY PROTEIN ENGINEERING
	Other Details - Source	:	CDNA OBTAINED BY SITE-SPECIFIC MUTAGENESIS OF WILD-TYPE CANINE RAN CDNA AS DESCRIBED IN PUBLICATION
	Strain	:	FAMILIARIS
	Synonym	:	TC4

		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, 8)

No.	Name	Count	Type	Full Name
1	GDP	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:24 , GDP A:704 , HOH A:705 , HOH A:706 , HOH A:707 , HOH A:708	BINDING SITE FOR RESIDUE MG A 700
2	AC2	SOFTWARE	THR B:24 , GDP B:705 , HOH B:706 , HOH B:707 , HOH B:708 , HOH B:709	BINDING SITE FOR RESIDUE MG B 701
3	AC3	SOFTWARE	THR C:24 , GDP C:706 , HOH C:707 , HOH C:708 , HOH C:709 , HOH C:710	BINDING SITE FOR RESIDUE MG C 702
4	AC4	SOFTWARE	THR D:24 , GDP D:707 , HOH D:708 , HOH D:709 , HOH D:710 , HOH D:711	BINDING SITE FOR RESIDUE MG D 703
5	AC5	SOFTWARE	GLY A:20 , THR A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , ASN A:122 , LYS A:123 , ASP A:125 , SER A:150 , ALA A:151 , LYS A:152 , MG A:700 , HOH A:705 , HOH A:706 , HOH A:708 , HOH A:720 , HOH A:749 , LYS C:127	BINDING SITE FOR RESIDUE GDP A 704
6	AC6	SOFTWARE	GLY B:20 , THR B:21 , GLY B:22 , LYS B:23 , THR B:24 , THR B:25 , ASN B:122 , LYS B:123 , ASP B:125 , SER B:150 , ALA B:151 , LYS B:152 , MG B:701 , HOH B:706 , HOH B:707 , HOH B:709	BINDING SITE FOR RESIDUE GDP B 705
7	AC7	SOFTWARE	HOH A:757 , GLY C:20 , THR C:21 , GLY C:22 , LYS C:23 , THR C:24 , THR C:25 , ASN C:122 , LYS C:123 , ASP C:125 , ALA C:151 , LYS C:152 , MG C:702 , HOH C:707 , HOH C:708 , HOH C:710 , HOH C:733	BINDING SITE FOR RESIDUE GDP C 706
8	AC8	SOFTWARE	ASP B:190 , GLY D:20 , THR D:21 , GLY D:22 , LYS D:23 , THR D:24 , THR D:25 , ASN D:122 , LYS D:123 , ASP D:125 , SER D:150 , ALA D:151 , LYS D:152 , MG D:703 , HOH D:708 , HOH D:709 , HOH D:711 , HOH D:766	BINDING SITE FOR RESIDUE GDP D 707

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAN	PS51418	small GTPase Ran family profile.	RAN_CANLF	4-168	3	B:4-168 C:4-168 D:4-168

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAN	PS51418	small GTPase Ran family profile.	RAN_CANLF	4-168	0	- - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAN	PS51418	small GTPase Ran family profile.	RAN_CANLF	4-168	1	B:4-168 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAN	PS51418	small GTPase Ran family profile.	RAN_CANLF	4-168	1	- C:4-168 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAN	PS51418	small GTPase Ran family profile.	RAN_CANLF	4-168	1	- - D:4-168

(no "Exon" information available for 3RAN)

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:201
 aligned with RAN_CANLF | P62825 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
            RAN_CANLF     5 GEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQ 205
               SCOP domains d3rana_ A: Ran                                                                                                                                                                                            SCOP domains
               CATH domains 3ranA00 A:5-205 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....hhhhhhh.hhhhh..eeehhh.eeeeeeeeee..eeeeeeeeee..........hhhh....eeeeeee...hhhhh.hhhhhhhhhhhh...eeeeeee..........hhh.........eeeee.hhh.....hhhhhhhhhhh.....................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAN  PDB: - UniProt: 4-168                                                                                                                                          ------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ran A   5 GEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQ 205
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with RAN_CANLF | P62825 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
            RAN_CANLF     4 QGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTT 207
               SCOP domains d3ranb_ B: Ran                                                                                                                                                                                               SCOP domains
               CATH domains 3ranB00 B:4-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhh.hhhhh..eee....eeeeeeeeee..eeeeeeeeee..........hhhh....eeeeeee...hhhhh.hhhhhhhhhhh....eeeeeee..........hhh........eeeeee.hhh...hhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE RAN  PDB: B:4-168 UniProt: 4-168                                                                                                                                     --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ran B   4 QGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTT 207
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain C from PDB  Type:PROTEIN  Length:203
 aligned with RAN_CANLF | P62825 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
            RAN_CANLF     4 QGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQT 206
               SCOP domains d3ranc_ C: Ran                                                                                                                                                                                              SCOP domains
               CATH domains 3ranC00 C:4-206 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhh.hhhhh..eeehhh.eeeeeeeeee..eeeeeeeeee..........hhhh....eeeeeee...hhhhh.hhhhhhhhhhhh...eeeeeee..........hhhhhh.....eeeee..hhh.....hhhhhhhhhhh.....................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAN  PDB: C:4-168 UniProt: 4-168                                                                                                                                     -------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ran C   4 QGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQT 206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain D from PDB  Type:PROTEIN  Length:203
 aligned with RAN_CANLF | P62825 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
            RAN_CANLF     4 QGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQT 206
               SCOP domains d3rand_ D: Ran                                                                                                                                                                                              SCOP domains
               CATH domains 3ranD00 D:4-206 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhh.hhhhh..eeehhh.eeeeeeeeee..eeeeeeeeee..........hhhh....eeeeeee...hhhhh.hhhhhhhhhhh....eeeeeee..........hhhh.......eeeee..hhh.....hhhhhhhhhhh.....................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAN  PDB: D:4-168 UniProt: 4-168                                                                                                                                     -------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ran D   4 QGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQT 206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Legend:		→ Mismatch	(orange background)
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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: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: Ran (37)

Dog (Canis familiaris) [TaxId: 9615] (8)

1a	d3rana_	A:
1b	d3ranb_	B:
1c	d3ranc_	C:
1d	d3rand_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Dog (Canis lupus familiaris) (19)

1a	3ranB00	B:4-207
1b	3ranC00	C:4-206
1c	3ranD00	D:4-206
1d	3ranA00	A:5-205

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RAN_CANLF | P62825)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0006913	nucleocytoplasmic transport	The directed movement of molecules between the nucleus and the cytoplasm.
	GO:0006606	protein import into nucleus	The directed movement of a protein from the cytoplasm to the nucleus.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000054	ribosomal subunit export from nucleus	The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
	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.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	RAN_CANLF \| P62825	:	1a2k 1byu 1qg2 1qg4 1wa5 2bku 3a6p 3w3z 5bxq

(no "Related Entries Specified in the PDB File" available for 3RAN)

Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

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