1ZBD - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A

Authors :   C. Ostermeier, A. T. Brunger

Date :   06 Nov 98 (Deposition) - 02 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)

Keywords :   G Protein, Effector, Rabcdr, Synaptic Exocytosis, Rab Protein, Rab3A, Rabphilin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Ostermeier, A. T. Brunger
Structural Basis Of Rab Effector Specificity: Crystal Structure Of The Small G Protein Rab3A Complexed With The Effector Domain Of Rabphilin-3A.
Cell(Cambridge, Mass. ) V. 96 363 1999
PubMed-ID: 10025402 | Reference-DOI: 10.1016/S0092-8674(00)80549-8
(for further references see the PDB file header)

Molecule 1 - RABPHILIN-3A
	Cellular Location	:	SYNAPTIC VESICLES
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	469008
	Expression System Variant	:	(DE3)
	Fragment	:	19-217
	Mutation	:	YES
	Organ	:	BRAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	RAS-RELATED PROTEIN RAB-3A
	Tissue	:	NEURONS

Molecule 2 - RABPHILIN-3A
	Cellular Location	:	SYNAPTIC VESICLES
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	469008
	Expression System Variant	:	(DE3)
	Fragment	:	40-170, EFFECTOR DOMAIN
	Mutation	:	YES
	Organ	:	BRAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	COMPLEXED WITH GUANOSINE-5'-TRIPHOSPHATE
	Synonym	:	RAS-RELATED PROTEIN RAB-3A
	Tissue	:	NEURONS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 15)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 24)

No.	Name	Count	Type	Full Name
1	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:111 , CYS B:114 , CYS B:137 , CYS B:140	BINDING SITE FOR RESIDUE ZN B 300
2	AC2	SOFTWARE	CYS B:94 , CYS B:97 , CYS B:119 , CYS B:122	BINDING SITE FOR RESIDUE ZN B 301
3	AC3	SOFTWARE	THR A:36 , THR A:54 , GTP A:303	BINDING SITE FOR RESIDUE MG A 302
4	AC4	SOFTWARE	ASN A:30 , SER A:31 , SER A:32 , VAL A:33 , GLY A:34 , LYS A:35 , THR A:36 , SER A:37 , THR A:48 , PRO A:49 , ALA A:50 , PHE A:51 , SER A:53 , THR A:54 , GLY A:80 , ASN A:135 , LYS A:136 , ASP A:138 , MSE A:139 , SER A:165 , ALA A:166 , LYS A:167 , MG A:302	BINDING SITE FOR RESIDUE GTP A 303
5	ZN1	UNKNOWN	CYS B:94 , CYS B:97 , CYS B:119 , CYS B:122	ZN-BINDING RESIDUES FOR ZN 301
6	ZN2	UNKNOWN	CYS B:111 , CYS B:114 , CYS B:137 , CYS B:140	ZN-BINDING RESIDUES FOR ZN 300

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

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

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	RAB3A_RAT	18-220	1	A:19-192
2	ZF_FYVE	PS50178	Zinc finger FYVE/FYVE-related type profile.	RP3A_RAT	88-145	1	B:88-145

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	RAB3A_RAT	18-220	1	A:19-192
2	ZF_FYVE	PS50178	Zinc finger FYVE/FYVE-related type profile.	RP3A_RAT	88-145	1	B:88-145

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	RAB3A_RAT	18-220	2	A:19-192
2	ZF_FYVE	PS50178	Zinc finger FYVE/FYVE-related type profile.	RP3A_RAT	88-145	2	B:88-145

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000026391	1	ENSRNOE00000426276	chr16:19193874-19193767	108	RAB3A_RAT	-	0	0	-	-
1.2b	ENSRNOT00000026391	2b	ENSRNOE00000188693	chr16:19192725-19192498	228	RAB3A_RAT	1-76	76	1	A:16-76	61
1.5	ENSRNOT00000026391	5	ENSRNOE00000291604	chr16:19192016-19191898	119	RAB3A_RAT	77-116	40	1	A:77-116	40
1.6	ENSRNOT00000026391	6	ENSRNOE00000188854	chr16:19191277-19191153	125	RAB3A_RAT	116-158	43	1	A:116-158	43
1.8	ENSRNOT00000026391	8	ENSRNOE00000238253	chr16:19190563-19189768	796	RAB3A_RAT	158-220	63	1	A:158-192	35

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:177
 aligned with RAB3A_RAT | P63012 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:177
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       
            RAB3A_RAT    16 DQNFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVICEKMSESLD 192
               SCOP domains d1zbda_ A: Rab3a                                                                                                                                                                  SCOP domains
               CATH domains 1zbdA00 A:16-192 P-loop containing nucleotide triphosphate hydrolases                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.......hhhhhhhhh.............eeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh......eeeeee...........hhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RAB  PDB: A:19-192 UniProt: 18-220                                                                                                                                              PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:16-76 UniProt: 1-76 [INCOMPLETE]           Exon 1.5  PDB: A:77-116 UniProt: 77-116 -----------------------------------------Exon 1.8  PDB: A:158-192            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:116-158 UniProt: 116-158  ---------------------------------- Transcript 1 (2)
                 1zbd A  16 SHmFDYmFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGLERYRTITTAYYRGAmGFILmYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDmEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVICEKmSESLD 192
                              |   | 25        35        45        55        65        75        85        95|    | 105       115       125       135   |   145       155       165       175       185 |     
                              |   |                                                                        96-MSE|                                   139-MSE                                         187-MSE 
                             18-MSE                                                                            101-MSE                                                                                       
                                 22-MSE

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with RP3A_RAT | P47709 from UniProtKB/Swiss-Prot  Length:684

    Alignment length:124
                                    53        63        73        83        93       103       113       123       133       143       153       163    
             RP3A_RAT    44 EELTDEEKEIINRVIARAEKMETMEQERIGRLVDRLETMRKNVAGDGVNRCILCGEQLGMLGSACVVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLEQREVWKRSGAWFFKGFPKQVLPQPM 167
               SCOP domains d1zbdb_ B: Effector domain of rabphilin-3a                                                                                   SCOP domains
               CATH domains 1zbdB00 B:44-166 Zinc/RING finger domain, C3HC4 (zinc finger)                                                              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................eee......eee...eee.........eeehhhhhhhhhhhh..hhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------ZF_FYVE  PDB: B:88-145 UniProt: 88-145                    ---------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zbd B  44 EELTDEEKEIINRVIARAEKmETmEQERIGRLVDRLETmRKNVAGDGVNRCILCGEQLGmLGSASVVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLEQREVWKRSGAWFFKGFPKQVLPQPm 167
                                    53        63|  |    73        83        93       103       113       123       133       143       153       163   |
                                               64-MSE            82-MSE              103-MSE                                                         167-MSE
                                                  67-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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Herpes Virus-1 (49)

Homologous Superfamily: Zinc/RING finger domain, C3HC4 (zinc finger) (47)

Norway rat (Rattus norvegicus) (1)

1zbdB00

B:44-166

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

Topology: Rossmann fold (7312)

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

Norway rat (Rattus norvegicus) (38)

1zbdA00

A:16-192

(no "Pfam Domain" information available for 1ZBD)

Asymmetric Unit(hide GO term definitions)

Chain A (RAB3A_RAT | P63012)

molecular function
	GO:0001671	ATPase activator activity	Binds to and increases the ATP hydrolysis activity of an ATPase.
	GO:0051117	ATPase binding	Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
	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:0051020	GTPase binding	Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
	GO:0031489	myosin V binding	Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport.
	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:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0032482	Rab protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rab family of proteins switching to a GTP-bound active state.
	GO:0007409	axonogenesis	De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
	GO:0061670	evoked neurotransmitter secretion	Neurotransmitter secretion that occurs in the presence of the action of a secretagogue or a presynaptic action potential.
	GO:0006887	exocytosis	A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
	GO:0030324	lung development	The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
	GO:0048790	maintenance of presynaptic active zone structure	A process which maintains the organization and the arrangement of proteins at the active zone to ensure the fusion and docking of vesicles and the release of neurotransmitters.
	GO:0007005	mitochondrion organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
	GO:0007274	neuromuscular synaptic transmission	The process of synaptic transmission from a neuron to a muscle, across a synapse.
	GO:0032781	positive regulation of ATPase activity	Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
	GO:1903307	positive regulation of regulated secretory pathway	Any process that activates or increases the frequency, rate or extent of regulated secretory pathway.
	GO:0009791	post-embryonic development	The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
	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:0017157	regulation of exocytosis	Any process that modulates the frequency, rate or extent of exocytosis.
	GO:0048172	regulation of short-term neuronal synaptic plasticity	A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
	GO:0031630	regulation of synaptic vesicle fusion to presynaptic active zone membrane	Any process that modulates the frequency, rate or extent of synaptic vesicle fusion to the presynaptic membrane.
	GO:0003016	respiratory system process	A system process carried out by the organs and tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
	GO:0051602	response to electrical stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus.
	GO:0050975	sensory perception of touch	The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach).
	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:0016079	synaptic vesicle exocytosis	Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
	GO:0016188	synaptic vesicle maturation	Steps required to form an initiated synaptic vesicle into a fully formed and transmissible synaptic vesicle.
	GO:0036465	synaptic vesicle recycling	The trafficking of synaptic vesicles from the pre-synaptic membrane so the vesicle can dock and prime for another round of exocytosis and neurotransmitter release. Recycling occurs after synaptic vesicle exocytosis, and is necessary to replenish presynaptic vesicle pools, sustain transmitter release and preserve the structural integrity of the presynaptic membrane. Recycling can occur following transient fusion with the presynaptic membrane (kiss and run), or via endocytosis of presynaptic membrane.
	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:0001669	acrosomal vesicle	A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	GO:0043229	intracellular organelle	Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. 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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
	GO:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

Chain B (RP3A_RAT | P47709)

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:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005544	calcium-dependent phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
	GO:0030276	clathrin binding	Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
	GO:0070679	inositol 1,4,5 trisphosphate binding	Interacting selectively and non-covalently with inositol 1,4,5 trisphosphate.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042301	phosphate ion binding	Interacting selectively and non-covalently with phosphate.
	GO:0005546	phosphatidylinositol-4,5-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008430	selenium binding	Interacting selectively and non-covalently with selenium (Se).
	GO:0019905	syntaxin binding	Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0048791	calcium ion-regulated exocytosis of neurotransmitter	The release of a neurotransmitter into the synaptic cleft by exocytosis of synaptic vesicles, where the release step is dependent on a rise in cytosolic calcium ion levels.
	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: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:0017158	regulation of calcium ion-dependent exocytosis	Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis.
	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:0006906	vesicle fusion	Fusion of the membrane of a transport vesicle with its target membrane.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	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:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
	GO:0030672	synaptic vesicle membrane	The lipid bilayer surrounding a synaptic vesicle.

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	1zbd
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	RP3A_RAT \| P47709
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	RAB3A_RAT \| P63012	:	3rab
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(no "Related Entries Specified in the PDB File" available for 1ZBD)

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (4, 15)

Sites (6, 6)

SS Bonds (0, 0)

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