1Z0J - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF GTP-BOUND RAB22Q64L GTPASE IN COMPLEX WITH THE MINIMAL RAB BINDING DOMAIN OF RABENOSYN-5

Authors :   S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright

Date :   01 Mar 05 (Deposition) - 26 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.32

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rab Effector, Rab Gtpase, Rab22 Gtpase, Rabenosyn, Endosomal Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Structural Basis Of Family-Wide Rab Gtpase Recognition By Rabenosyn-5.
Nature V. 436 415 2005
PubMed-ID: 16034420 | Reference-DOI: 10.1038/NATURE03798

Molecule 1 - RAS-RELATED PROTEIN RAB-22A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET28A
	Expression System Strain	:	BL21 (DE3) CODON PLUS-RIL CELLS
	Expression System Taxid	:	562
	Expression System Vector Type	:	6XHIS FUSION, PET
	Gene	:	RAB22A, RAB22
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	RAB-22

Molecule 2 - FYVE-FINGER-CONTAINING RAB5 EFFECTOR PROTEIN RABENOSYN-5
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET15B
	Expression System Taxid	:	562
	Fragment	:	MINIMAL RAB BINDING DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:19 , THR A:37 , GTP A:500 , HOH A:1004 , HOH A:1006	BINDING SITE FOR RESIDUE MG A 400
2	AC2	SOFTWARE	THR A:14 , GLY A:15 , VAL A:16 , GLY A:17 , LYS A:18 , SER A:19 , SER A:20 , PHE A:30 , ASP A:31 , PRO A:32 , ILE A:34 , PRO A:36 , THR A:37 , GLY A:63 , ASN A:118 , LYS A:119 , ASP A:121 , SER A:148 , ALA A:149 , LYS A:150 , MG A:400 , HOH A:1004 , HOH A:1006 , HOH A:1008 , HOH A:1011 , HOH A:1013 , HOH A:1044 , HOH A:1135	BINDING SITE FOR RESIDUE GTP A 500
3	AC3	SOFTWARE	LYS A:89 , ARG A:104 , PRO A:108 , PRO A:109 , ILE A:111 , ILE A:140 , GOL A:1002	BINDING SITE FOR RESIDUE TRS A 1001
4	AC4	SOFTWARE	ASP A:86 , THR A:88 , LYS A:89 , ARG A:104 , PRO A:109 , LYS A:119 , TRS A:1001 , HOH A:1026	BINDING SITE FOR RESIDUE GOL A 1002

(no "SS Bond" information available for 1Z0J)

(no "Cis Peptide Bond" information available for 1Z0J)

(no "SAP(SNP)/Variant" information available for 1Z0J)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	RB22A_MOUSE	1-194	1	A:2-168

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000253699	1b	ENSE00001426996	chr3:15140655-15140542	114	RBNS5_HUMAN	-	0	0	-	-
1.2	ENST00000253699	2	ENSE00001400873	chr3:15139781-15139626	156	RBNS5_HUMAN	-	0	0	-	-
1.3	ENST00000253699	3	ENSE00001399837	chr3:15138217-15138042	176	RBNS5_HUMAN	-	0	0	-	-
1.4b	ENST00000253699	4b	ENSE00002148188	chr3:15137795-15137480	316	RBNS5_HUMAN	1-50	50	0	-	-
1.6	ENST00000253699	6	ENSE00001735576	chr3:15132046-15131906	141	RBNS5_HUMAN	50-97	48	0	-	-
1.7b	ENST00000253699	7b	ENSE00001740707	chr3:15127468-15127368	101	RBNS5_HUMAN	97-130	34	0	-	-
1.8	ENST00000253699	8	ENSE00001646587	chr3:15126552-15126507	46	RBNS5_HUMAN	131-146	16	0	-	-
1.9	ENST00000253699	9	ENSE00001761956	chr3:15126403-15126242	162	RBNS5_HUMAN	146-200	55	0	-	-
1.10b	ENST00000253699	10b	ENSE00001748893	chr3:15124115-15123874	242	RBNS5_HUMAN	200-280	81	0	-	-
1.13	ENST00000253699	13	ENSE00001680530	chr3:15122309-15122239	71	RBNS5_HUMAN	281-304	24	0	-	-
1.14c	ENST00000253699	14c	ENSE00000901297	chr3:15119668-15119582	87	RBNS5_HUMAN	304-333	30	0	-	-
1.15	ENST00000253699	15	ENSE00000901296	chr3:15118671-15118569	103	RBNS5_HUMAN	333-367	35	0	-	-
1.16	ENST00000253699	16	ENSE00000901295	chr3:15117217-15117113	105	RBNS5_HUMAN	368-402	35	0	-	-
1.19e	ENST00000253699	19e	ENSE00001242854	chr3:15116437-15111580	4858	RBNS5_HUMAN	403-784	382	1	B:734-784	51

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:169
 aligned with RB22A_MOUSE | P35285 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
          RB22A_MOUSE     - -MALRELKVCLLGDTGVGKSSIVWRFVEDSFDPNINPTIGASFMTKTVQYQNELHKFLIWDTAGQERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVMERDAKDYADSIHAIFVETSAKNAININELFIEISRRIPS 168
               SCOP domains --d1z0ja1 A:2-168 Rab-22a                                                                                                                                                 SCOP domains
               CATH domains 1z0jA00 A:0-168 P-loop containing nucleotide triphosphate hydrolases                                                                                                      CATH domains
               Pfam domains -------Ras-1z0jA01 A:7-168                                                                                                                                                Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RAB  PDB: A:2-168 UniProt: 1-194                                                                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0j A   0 GSALRELKVCLLGDTGVGKSSIMWRFVEDSFDPNINPTIGASFMTKTVQYQNELHKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVMERDAKDYADSIHAIFVETSAKNAININELFIEISRRIPS 168
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

Chain B from PDB  Type:PROTEIN  Length:51
 aligned with RBNS5_HUMAN | Q9H1K0 from UniProtKB/Swiss-Prot  Length:784

    Alignment length:51
                                   743       753       763       773       783 
          RBNS5_HUMAN   734 IEEELLLQQIDNIKAYIFDAKQCGRLDEVEVLTENLRELKHTLAKQKGGTD 784
               SCOP domains d1z0jb1 B:734-784                                   SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains -----Rbsn-1z0jB01 B:739-780                    ---- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
               Transcript 1 Exon 1.19e  PDB: B:734-784 UniProt: 403-784         Transcript 1
                 1z0j B 734 IEEELLLQQIDNIKAYIFDAKQCGRLDEVEVLTENLRELKHTLAKQKGGTD 784
                                   743       753       763       773       783

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: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

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

House mouse (Mus musculus) (47)

1z0jA00

A:0-168

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Mus musculus (Mouse) (16)

Ras-1z0jA01

A:7-168

Clan: no clan defined [family: Rbsn] (2)

Family: Rbsn (2)

Homo sapiens (Human) (2)

Rbsn-1z0jB01

B:739-780

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RB22A_MOUSE | P35285)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	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.
	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:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0007032	endosome organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
	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:0097494	regulation of vesicle size	Any process that modulates the size of a vesicle.
	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:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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.
	GO:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	GO:0030670	phagocytic vesicle membrane	The lipid bilayer surrounding a phagocytic vesicle.
	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:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Chain B (RBNS5_HUMAN | Q9H1K0)

molecular function
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	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).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006895	Golgi to endosome transport	The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes.
	GO:0090160	Golgi to lysosome transport	The directed movement of substances from the Golgi to lysosomes.
	GO:0006896	Golgi to vacuole transport	The directed movement of substances from the Golgi to the vacuole.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0034498	early endosome to Golgi transport	The directed movement of substances from early endosomes to the Golgi.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0016197	endosomal transport	The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
	GO:0034058	endosomal vesicle fusion	The homotypic fusion of endocytic vesicles to form or add to an early endosome.
	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:1903358	regulation of Golgi organization	Any process that modulates the frequency, rate or extent of Golgi organization.
	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.
	GO:0000011	vacuole inheritance	The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.
cellular component
	GO:0010009	cytoplasmic side of endosome membrane	The side (leaflet) of the endosome membrane that faces the cytoplasm.
	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:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1z0j
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(no "Related Entries Specified in the PDB File" available for 1Z0J)

Description

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Ligands, Modified Residues, Ions (4, 4)

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