3KXC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   MUTANT TRANSPORT PROTEIN

Authors :   D. Kummel, U. Heinemann

Date :   02 Dec 09 (Deposition) - 21 Apr 10 (Release) - 07 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Heterodimer, Endoplasmic Reticulum, Er-Golgi Transport, Golgi Apparatus, Lipoprotein, Palmitate, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kummel, J. Walter, M. Heck, U. Heinemann, M. Veit
Characterization Of The Self-Palmitoylation Activity Of The Transport Protein Particle Component Bet3
Cell. Mol. Life Sci. V. 67 2653 2010
PubMed-ID: 20372964 | Reference-DOI: 10.1007/S00018-010-0358-Y

Molecule 1 - TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BET3, BET3 HOMOLOG

Molecule 2 - TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TPC6B

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PLM	1	Ligand/Ion	PALMITIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:67 , VAL A:77 , LEU A:131 , LEU C:6	BINDING SITE FOR RESIDUE PLM A 181

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

Asymmetric/Biological Unit

No.	Residues
1	Leu A:118	-	Pro A:119
2	Met C:146	-	Pro C:147

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

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

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000330149	1c	ENSE00001846910	chr14:39639526-39639219	308	TPC6B_HUMAN	1-27	27	1	C:2-27 (gaps)	26
1.2a	ENST00000330149	2a	ENSE00001298290	chr14:39628754-39628687	68	TPC6B_HUMAN	28-50	23	1	C:28-50	23
1.2c	ENST00000330149	2c	ENSE00001318696	chr14:39627606-39627489	118	TPC6B_HUMAN	50-89	40	1	C:50-89 (gaps)	40
1.3	ENST00000330149	3	ENSE00001334158	chr14:39623498-39623415	84	TPC6B_HUMAN	90-117	28	1	C:90-117 (gaps)	28
1.4	ENST00000330149	4	ENSE00001297356	chr14:39621043-39620950	94	TPC6B_HUMAN	118-149	32	1	C:118-149	32
1.5b	ENST00000330149	5b	ENSE00001869808	chr14:39619585-39617016	2570	TPC6B_HUMAN	149-158	10	1	C:149-158	10

2.1c	ENST00000373166	1c	ENSE00001889875	chr1:36615070-36614938	133	TPPC3_HUMAN	1-14	14	0	-	-
2.2b	ENST00000373166	2b	ENSE00001718673	chr1:36605767-36605670	98	TPPC3_HUMAN	15-47	33	1	A:16-47	32
2.3a	ENST00000373166	3a	ENSE00000766274	chr1:36605420-36605321	100	TPPC3_HUMAN	47-80	34	1	A:47-80	34
2.5b	ENST00000373166	5b	ENSE00000766275	chr1:36603579-36603397	183	TPPC3_HUMAN	81-141	61	1	A:81-141	61
2.5g	ENST00000373166	5g	ENSE00001459692	chr1:36602923-36602173	751	TPPC3_HUMAN	142-180	39	1	A:142-171	30

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:156
 aligned with TPPC3_HUMAN | O43617 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:156
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165      
          TPPC3_HUMAN    16 SELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRI 171
               SCOP domains d3kxca_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eee.......eeeeee....................hhhhhhhhhhhhhh..eeeeeeeeehhhhh...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.2b  PDB: A:16-47         ---------------------------------Exon 2.5b  PDB: A:81-141 UniProt: 81-141                     Exon 2.5g  PDB: A:142-171      Transcript 2 (1)
           Transcript 2 (2) -------------------------------Exon 2.3a  PDB: A:47-80           ------------------------------------------------------------------------------------------- Transcript 2 (2)
                 3kxc A  16 SELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRAHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRI 171
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165

Chain C from PDB  Type:PROTEIN  Length:136
 aligned with TPC6B_HUMAN | Q86SZ2 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
          TPC6B_HUMAN     2 ADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENMGFRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQMSAGKQYLEHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQKL 158
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhh....eeee....eeeeee.......-----------hhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c UniProt: 1-27   Exon 1.2a  PDB: C:28-50---------------------------------------Exon 1.3 UniProt: 90-117    Exon 1.4  PDB: C:118-149        --------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.2c  PDB: C:50-89 (gaps)          -----------------------------------------------------------Exon 1.5b  Transcript 1 (2)
                 3kxc C   2 ADEALFLLLHNEMVSG------QGEVENGRCITKLENMGFRVGQGLIERFTK----FKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLT-----------ASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQKL 158
                                    11     |   -  |     31        41        51 |    | 61        71        81        91       101 |       -   |   121       131       141       151       
                                          17     24                           53   58                                          103         115

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ligand-binding domain in the NO signalling and Golgi transport (29)

Superfamily: Ligand-binding domain in the NO signalling and Golgi transport (29)

Family: TRAPP components (11)

Protein domain: automated matches (7)

Human (Homo sapiens) [TaxId: 9606] (4)

d3kxca_

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

(no "Pfam Domain" information available for 3KXC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TPPC3_HUMAN | O43617)

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).
biological process
	GO:0048208	COPII vesicle coating	The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
	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: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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

Chain C (TPC6B_HUMAN | Q86SZ2)

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).
biological process
	GO:0048208	COPII vesicle coating	The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
	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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

Asymmetric/Biological Unit
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		Met C:146 - Pro C:147	[ RasMol ]

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	3kxc
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	TPPC3_HUMAN \| O43617
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UniProtKB/Swiss-Prot
	TPC6B_HUMAN \| Q86SZ2	:	2bjn 2cfh
	TPPC3_HUMAN \| O43617	:	1sz7 2c0j 2cfh

2cfh	STRUCTURE OF THE BET3-TPC6B CORE OF TRAPP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (10, 10)

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SCOP Domains (1, 1)

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Gene Ontology (10, 18)

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Related Entries Specified in the PDB File