3MKR - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YEAST ALPHA/EPSILON-COP SUBCOMPLEX OF THE COPI VESICULAR COAT

Authors :   C. Lee, J. Goldberg

Date :   15 Apr 10 (Deposition) - 14 Jul 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Tetratricopeptide Repeats (Tpr), Beta-Hairpin, Alpha-Solenoid, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Lee, J. Goldberg
Structure Of Coatomer Cage Proteins And The Relationship Among Copi, Copii, And Clathrin Vesicle Coats.
Cell(Cambridge, Mass. ) V. 142 123 2010
PubMed-ID: 20579721 | Reference-DOI: 10.1016/J.CELL.2010.05.030

Molecule 1 - COATOMER SUBUNIT EPSILON
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 17-307
	Gene	:	COPE, COPE1
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	EPSILON-COAT PROTEIN, EPSILON-COP

Molecule 2 - COATOMER SUBUNIT ALPHA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 905-1224
	Gene	:	COPA
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ALPHA-COAT PROTEIN, ALPHA-COP, HEP-COP, HEPCOP, XENIN, XENOPSIN-RELATED PEPTIDE, PROXENIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3MKR)

(no "Site" information available for 3MKR)

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

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

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

(no "PROSITE Motif" information available for 3MKR)

(no "Exon" information available for 3MKR)

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:291
 aligned with COPE_BOVIN | Q28104 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:291
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306 
          COPE_BOVIN     17 DELFDVKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKPSSAPELQAVRMFAEYLASDSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHRSHPFIKEYRAKENDFDRLVLQYAPS  307
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Coatomer_E-3mkrA01 A:17-305                                                                                                                                                                                                                                                                      -- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mkr A   17 DELFDVKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHRSHPFIKEYRAKENDFDRLVLQYAPS  307
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with COPA_BOVIN | Q27954 from UniProtKB/Swiss-Prot  Length:1224

    Alignment length:320
                                   914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224
          COPA_BOVIN    905 GFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVTQFGPYKQLFLQTYARGRTTYQALPCLPSMYGYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLVVDNKQEIAEAQQLITICREYIVGLSMETERKKLPKETLEQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFRTAAAFARRLLELGPKPEVAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQICKVTTVTEIGKDVIGLRISPLQFR 1224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains COPI_C-3mkrB01 B:905-1224                                                                                                                                                                                                                                                                                                        Pfam domains
         Sec.struct. author ..........hhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhh...eee........eee....................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............................ee......eehhhhh.....................hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mkr B  905 GFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVTQFGPYKQLFLQTYARGRTTYQALPCLPSMYGYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLVVDNKQEIAEAQQLITICREYIVGLSMETERKKLPKETLEQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFRTAAAFARRLLELGPKPEVAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQICKVTTVTEIGKDVIGLRISPLQFR 1224
                                   914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224

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 3MKR)

(no "CATH Domain" information available for 3MKR)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TPR (230)

Family: Coatomer_E (3)

Bos taurus (Bovine) (1)

Coatomer_E-3mkrA01

A:17-305

Clan: no clan defined [family: COPI_C] (3)

Family: COPI_C (3)

Bos taurus (Bovine) (1)

COPI_C-3mkrB01

B:905-1224

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (COPE_BOVIN | Q28104)

molecular function
	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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
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: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: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:0006890	retrograde vesicle-mediated transport, Golgi to ER	The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
	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: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:0030126	COPI vesicle coat	One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state.
	GO:0030137	COPI-coated vesicle	A vesicle with a coat formed of the COPI coat complex proteins. COPI-coated vesicles are found associated with Golgi membranes at steady state, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and possibly also in intra-Golgi transport.
	GO:0030663	COPI-coated vesicle membrane	The lipid bilayer surrounding a COPI-coated vesicle.
	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:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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: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.

Chain B (COPA_BOVIN | Q27954)

molecular function
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
	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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
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: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: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:0006890	retrograde vesicle-mediated transport, Golgi to ER	The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
	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: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:0030126	COPI vesicle coat	One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state.
	GO:0030663	COPI-coated vesicle membrane	The lipid bilayer surrounding a COPI-coated vesicle.
	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:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030117	membrane coat	Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.

Asymmetric/Biological Unit
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	3mkr
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	COPA_BOVIN \| Q27954
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	COPE_BOVIN \| Q28104
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