2CM6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN3A

Authors :   C. Schlicker, P. Montaville, G. M. Sheldrick, S. Becker

Date :   04 May 06 (Deposition) - 04 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Protein Transport, Zinc-Finger, Rabphilin3A, Ca2+ Binding, Metal-Binding, Synaptic Exocytosis, C2A-C2B Linker Fragment, C2B, Zinc, Synapse, C2 Domain, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Montaville, C. Schlicker, A. Leonov, M. Zweckstetter, G. M. Sheldrick, S. Becker
The C2A-C2B Linker Defines The High Affinity Ca2+ Binding Mode Of Rabphilin-3A.
J. Biol. Chem. V. 282 5015 2007
PubMed-ID: 17166855 | Reference-DOI: 10.1074/JBC.M606746200

Molecule 1 - RABPHILIN-3A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T-RABPHILIN3A-519-684
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PGEX-2T
	Fragment	:	C2B DOMAIN AND LINKER, RESIDUES 519-684
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	EXOPHILIN-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:571 , ASP A:577 , ASP A:631 , TYR A:632 , ASP A:633 , HOH A:2004	BINDING SITE FOR RESIDUE CA A1679
2	AC2	SOFTWARE	GLU A:530 , MET A:570 , ASP A:571 , ASP A:631 , ASP A:633 , ASP A:639	BINDING SITE FOR RESIDUE CA A1680
3	AC3	SOFTWARE	ASP B:1571 , ASP B:1577 , ASP B:1631 , TYR B:1632 , ASP B:1633 , HOH B:2004	BINDING SITE FOR RESIDUE CA B2679
4	AC4	SOFTWARE	GLU B:1530 , MET B:1570 , ASP B:1571 , ASP B:1631 , ASP B:1633 , ASP B:1639	BINDING SITE FOR RESIDUE CA B2680
5	AC5	SOFTWARE	HIS B:1594 , PHE B:1611 , PHE B:1612	BINDING SITE FOR RESIDUE PO4 B2681

(no "SS Bond" information available for 2CM6)

Asymmetric Unit

No.	Residues
1	Glu A:533	-	Arg A:534
2	Arg A:534	-	Ile A:535
3	Glu A:539	-	Glu A:540
4	Lys A:585	-	Pro A:586
5	Lys B:1585	-	Pro B:1586

(no "SAP(SNP)/Variant" information available for 2CM6)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	RP3A_RAT	397-488 557-645	2	- A:557-645 B:1557-1645

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	RP3A_RAT	397-488 557-645	1	- A:557-645 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	RP3A_RAT	397-488 557-645	1	- - B:1557-1645

(no "Exon" information available for 2CM6)

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:149
 aligned with RP3A_RAT | P47709 from UniProtKB/Swiss-Prot  Length:684

    Alignment length:155
                                   533       543       553       563       573       583       593       603       613       623       633       643       653       663       673     
            RP3A_RAT    524 MALYEEEQVERIGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNE  678
               SCOP domains d2cm6a_ A: a   utomated matches                                                                                                                             SCOP domains
               CATH domains 2cm6A00 A:52   4-678 C2- domain Calcium/lipid binding domain                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....---....eeeeeeeee....eeeeeeeeee............eeeeeeee.---...eee..........eeeeeeeee.hhhhhh..eeeeeeee.......eeeeeeeee...hhhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------C2  PDB: A:557-645 UniProt: 557-645                                                      --------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cm6 A  524 MALYEEEQVERI---EERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKP---KKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNE  678
                                   533 |   | 543       553       563       573       583  |   |593       603       613       623       633       643       653       663       673     
                                     535 539                                            586 590

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with RP3A_RAT | P47709 from UniProtKB/Swiss-Prot  Length:684

    Alignment length:154
                                   534       544       554       564       574       584       594       604       614       624       634       644       654       664       674    
            RP3A_RAT    525 ALYEEEQVERIGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNE  678
               SCOP domains d2cm6b_       B: automated matches                                                                                                                         SCOP domains
               CATH domains 2cm6B00       B:1525-1678 C2- domain Calcium/lipid binding domain                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..------....eeeeeeeee....eeeeeeeeee............eeeeeeee..hhhh.eee..........eeeeeeeee.hhhhhh..eeeeeeee.......eeeeeeee....hhhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------C2  PDB: B:1557-1645 UniProt: 557-645                                                    --------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cm6 B 1525 ALYEEEQV------EERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDPFVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSNDYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNE 1678
                                   | -    | 1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674    
                                1532   1539

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: C2 domain (Calcium/lipid-binding domain, CaLB) (148)

Family: Synaptotagmin-like (S variant) (38)

Protein domain: automated matches (6)

Norway rat (Rattus norvegicus) [TaxId: 10116] (4)

1a	d2cm6a_	A:
1b	d2cm6b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: C2- domain Calcium/lipid binding domain (78)

Rat (Rattus norvegicus) (8)

1a	2cm6B00	B:1525-1678
1b	2cm6A00	A:524-678

(no "Pfam Domain" information available for 2CM6)

Asymmetric Unit(hide GO term definitions)

Chain A,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.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:534 - Ile A:535	[ RasMol ]
		Glu A:533 - Arg A:534	[ RasMol ]
		Glu A:539 - Glu A:540	[ RasMol ]
		Lys A:585 - Pro A:586	[ RasMol ]
		Lys B:1585 - Pro B:1586	[ RasMol ]

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	2cm6
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UniProtKB/Swiss-Prot
	RP3A_RAT \| P47709	:	1zbd 2chd 2cm5 3rpb 4lt7 4np9 4ns0 5lo8 5lob 5low

1zbd	STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY : CRYSTALSTRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THEEFFECTOR DOMAIN OF RABPHILIN-3A
2chd	CRYSTAL STRUCTURE OF THE C2A DOMAIN OF RABPHILIN-3A
2cm5	CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN
3rpb	THE C2B-DOMAIN OF RABPHILIN: STRUCTURAL VARIATIONS IN A JANUS-FACED DOMAIN

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