2V8S - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   VTI1B HABC DOMAIN - EPSINR ENTH DOMAIN COMPLEX

Authors :   D. J. Owen, A. J. Mccoy, B. M. Collins, S. E. Miller

Date :   14 Aug 07 (Deposition) - 27 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.22

Chains :   Asym./Biol. Unit : E,V

Keywords :   Protein Transport, Cytoplasmic Vesicle, Lipid-Binding, Transmembrane, Phosphorylation, Alternative Splicing, Vti1B-Epsinr Complex, Cytoplasm, Transport, Endocytosis, Coiled Coil, Snare, Cargo, Adaptor, Vesicle, Membrane, Clathrin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. E. Miller, B. M. Collins, A. J. Mccoy, M. S. Robinson, D. J. Owen
A Snare-Adaptor Interaction Is A New Mode Of Cargo Recognition In Clathrin Coated Vesicles
Nature V. 450 570 2007
PubMed-ID: 18033301 | Reference-DOI: 10.1038/NATURE06353

Molecule 1 - CLATHRIN INTERACTOR 1
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	469008
	Fragment	:	ENTH, RESIDUES 20-166
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EPSINR, EPSIN-4, EPSIN-RELATED PROTEIN, ENTHOPROTIN, CLATHRIN-INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION, CLINT

Molecule 2 - VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1B
	Chains	:	V
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	469008
	Fragment	:	HABC DOMAIN, RESIDUES 1-96
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VTI1B, VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1, VTI1-RP1

		1	2
Asymmetric/Biological Unit	:	E	V

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER E:100 , GLU E:103 , HIS E:104 , HOH E:2057	BINDING SITE FOR RESIDUE GOL E1159
2	AC2	SOFTWARE	ASN E:33 , ASP E:34 , ARG E:67 , LYS E:133 , HOH E:2058 , HOH E:2059	BINDING SITE FOR RESIDUE GOL E1160
3	AC3	SOFTWARE	LYS E:122 , THR V:72 , PHE V:73 , PRO V:76 , MET V:77	BINDING SITE FOR RESIDUE GOL E1161
4	AC4	SOFTWARE	SER V:4 , GLU V:65 , TYR V:68	BINDING SITE FOR RESIDUE GOL V1095
5	AC5	SOFTWARE	GLY E:41 , GLN E:42 , ARG V:67	BINDING SITE FOR RESIDUE GOL V1096

(no "SS Bond" information available for 2V8S)

(no "Cis Peptide Bond" information available for 2V8S)

(no "SAP(SNP)/Variant" information available for 2V8S)

(no "PROSITE Motif" information available for 2V8S)

(no "Exon" information available for 2V8S)

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 E from PDB  Type:PROTEIN  Length:137
 aligned with EPN4_HUMAN | Q14677 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:137
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       
           EPN4_HUMAN    22 SEIESKVREATNDDPWGPSGQLMGEIAKATFMYEQFPELMNMLWSRMLKDNKKNWRRVYKSLLLLAYLIRNGSERVVTSAREHIYDLRSLENYHFVDEHGKDQGINIRQKVKELVEFAQDDDRLREERKKAKKNKDK 158
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v8sE00 E:22-158  [code=1.25.40.90, no name defined]                                                                                      CATH domains
               Pfam domains ENTH-2v8sE01 E:22-145                                                                                                       ------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8s E  22 SEIESKVREATNDDPWGPSGQLMGEIAKATFMYEQFPELMNMLWSRMLKDNKKNWRRVYKSLLLLAYLIRNGSERVVTSAREHIYDLRSLENYHFVDEHGKDQGINIRQKVKELVEFAQDDDRLREERKKAKKNKDK 158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151

Chain V from PDB  Type:PROTEIN  Length:93
 aligned with VTI1B_HUMAN | Q9UEU0 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
          VTI1B_HUMAN     2 ASSAASSEHFEKLHEIFRGLHEDLQGVPERLLGTAGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAPLSFRNPMMSKLRNYRKDLAKLHRE  94
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------V-SNARE-2v8sV01 V:18-94                                                       Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 2v8s V   2 ASSAASSEHFEKLHEIFRGLLEDLQGVPERLLGTAGTEEKKKLVRDFDEKQQEANETLAEMEEELRYAPLTFRNPMMSKLRNYRKDLAKLHRE  94
                                    11        21        31        41        51        61        71        81        91

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 '\|'

(no "SCOP Domain" information available for 2V8S)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Alpha Horseshoe (399)

Topology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat (320)

Homologous Superfamily: [code=1.25.40.90, no name defined] (33)

Human (Homo sapiens) (20)

2v8sE00

E:22-158

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ENTH_VHS (15)

Family: ENTH (4)

Homo sapiens (Human) (3)

ENTH-2v8sE01

E:22-145

Clan: Traffic (4)

Family: V-SNARE (3)

Homo sapiens (Human) (1)

V-SNARE-2v8sV01

V:18-94

Asymmetric/Biological Unit(hide GO term definitions)

Chain E (EPN4_HUMAN | Q14677)

molecular function
	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:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor 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:0030136	clathrin-coated vesicle	A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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: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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Chain V (VTI1B_HUMAN | Q9UEU0)

molecular function
	GO:0005484	SNAP receptor activity	Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
	GO:0000149	SNARE binding	Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
	GO:0019869	chloride channel inhibitor activity	Stops, prevents, or reduces the activity of a chloride channel.
	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:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0006896	Golgi to vacuole transport	The directed movement of substances from the Golgi to the vacuole.
	GO:0097352	autophagosome maturation	Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0006891	intra-Golgi vesicle-mediated transport	The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
	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:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0006623	protein targeting to vacuole	The process of directing proteins towards the vacuole, usually using signals contained within the protein.
	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:1903076	regulation of protein localization to plasma membrane	Any process that modulates the frequency, rate or extent of protein localization to plasma membrane.
	GO:0042147	retrograde transport, endosome to Golgi	The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
	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:0006904	vesicle docking involved in exocytosis	The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
	GO:0048280	vesicle fusion with Golgi apparatus	The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	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:0031201	SNARE complex	A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	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:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0055037	recycling endosome	An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma 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:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Asymmetric/Biological Unit
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	2v8s
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UniProtKB/Swiss-Prot
	EPN4_HUMAN \| Q14677	:	1xgw 2qy7

1xgw	THE CRYSTAL STRUCTURE OF HUMAN ENTHOPROTIN N -TERMINAL DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

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