2CFH - JenaLib

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Title :   STRUCTURE OF THE BET3-TPC6B CORE OF TRAPP

Authors :   D. Kummel, J. J. Muller, Y. Roske, N. Henke, U. Heinemann

Date :   21 Feb 06 (Deposition) - 12 Jul 06 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Protein Transport, Trapp Complex, Bet3, Tpc6, Vesicle Tethering, Transport, Er-Golgi Transport, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kummel, J. J. Muller, Y. Roske, N. Henke, U. Heinemann
Structure Of The Bet3-Tpc6B Core Of Trapp: Two Tpc6 Paralogs Form Trimeric Complexes With Bet3 And Mum2.
J. Mol. Biol. V. 361 22 2006
PubMed-ID: 16828797 | Reference-DOI: 10.1016/J.JMB.2006.06.012

Molecule 1 - TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-DUET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BET3 HOMOLOG

Molecule 2 - TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-DUET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TPC6B

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	PLM	2	Ligand/Ion	PALMITIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	PLM	1	Ligand/Ion	PALMITIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	PLM	1	Ligand/Ion	PALMITIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:56 , GLY A:66 , ARG A:67 , CYS A:68 , LEU A:131	BINDING SITE FOR RESIDUE PLM A1068
2	AC2	SOFTWARE	ILE B:56 , GLY B:66 , ARG B:67 , CYS B:68 , LEU B:131 , LEU B:139 , LEU D:6	BINDING SITE FOR RESIDUE PLM B1068

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

Asymmetric Unit

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

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

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

Asymmetric Unit (10, 20)

	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	2	C:2-27 D:2-27	26 26
1.2a	ENST00000330149	2a	ENSE00001298290	chr14:39628754-39628687	68	TPC6B_HUMAN	28-50	23	2	C:28-50 D:28-50	23 23
1.2c	ENST00000330149	2c	ENSE00001318696	chr14:39627606-39627489	118	TPC6B_HUMAN	50-89	40	2	C:50-89 D:50-89	40 40
1.3	ENST00000330149	3	ENSE00001334158	chr14:39623498-39623415	84	TPC6B_HUMAN	90-117	28	2	C:90-117 (gaps) D:90-117 (gaps)	28 28
1.4	ENST00000330149	4	ENSE00001297356	chr14:39621043-39620950	94	TPC6B_HUMAN	118-149	32	2	C:118-149 D:118-149	32 32
1.5b	ENST00000330149	5b	ENSE00001869808	chr14:39619585-39617016	2570	TPC6B_HUMAN	149-158	10	2	C:149-158 D:149-158	10 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	2	A:15-47 B:15-47	33 33
2.3a	ENST00000373166	3a	ENSE00000766274	chr1:36605420-36605321	100	TPPC3_HUMAN	47-80	34	2	A:47-80 B:47-80	34 34
2.5b	ENST00000373166	5b	ENSE00000766275	chr1:36603579-36603397	183	TPPC3_HUMAN	81-141	61	2	A:81-141 B:81-141	61 61
2.5g	ENST00000373166	5g	ENSE00001459692	chr1:36602923-36602173	751	TPPC3_HUMAN	142-180	39	2	A:142-176 B:142-176	35 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:162
 aligned with TPPC3_HUMAN | O43617 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:162
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          TPPC3_HUMAN    15 SSELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIEDNLP 176
               SCOP domains d2cfha_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains 2cfhA00 A:15-176 Trafficking protein particle complex subunit 3                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eee.......eeeeee....................hhhhhhhhhhhhhh..eeeeeeeeehhhhh...eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.2b  PDB: A:15-47          ---------------------------------Exon 2.5b  PDB: A:81-141 UniProt: 81-141                     Exon 2.5g  PDB: A:142-176           Transcript 2 (1)
           Transcript 2 (2) --------------------------------Exon 2.3a  PDB: A:47-80           ------------------------------------------------------------------------------------------------ Transcript 2 (2)
                 2cfh A  15 SSELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIEDNLP 176
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with TPPC3_HUMAN | O43617 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:162
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          TPPC3_HUMAN    15 SSELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIEDNLP 176
               SCOP domains d2cfhb_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains 2cfhB00 B:15-176 Trafficking protein particle complex subunit 3                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eee.......eeeeee....................hhhhhhhhhhhhhh..eeeeeeeeehhhhh...eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.2b  PDB: B:15-47          ---------------------------------Exon 2.5b  PDB: B:81-141 UniProt: 81-141                     Exon 2.5g  PDB: B:142-176           Transcript 2 (1)
           Transcript 2 (2) --------------------------------Exon 2.3a  PDB: B:47-80           ------------------------------------------------------------------------------------------------ Transcript 2 (2)
                 2cfh B  15 SSELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIEDNLP 176
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain C from PDB  Type:PROTEIN  Length:151
 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 .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeee....eeeeee........------...hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: C:2-27    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 UniProt: 50-89  -----------------------------------------------------------Exon 1.5b  Transcript 1 (2)
                 2cfh C   2 ADEALFLLLHNEMVSGVYKSAEQGEVENGRcITKLENMGFRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQ------YLEHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQKL 158
                                    11        21        31|       41        51        61        71        81        91       101  |    111       121       131       141       151       
                                                         32-CSO                                                                 104    111

Chain D from PDB  Type:PROTEIN  Length:152
 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 .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeee....eeeeee.........-----...hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: D:2-27    Exon 1.2a  PDB: D:28-50---------------------------------------Exon 1.3 UniProt: 90-117    Exon 1.4  PDB: D:118-149        --------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.2c  PDB: D:50-89 UniProt: 50-89  -----------------------------------------------------------Exon 1.5b  Transcript 1 (2)
                 2cfh D   2 ADEALFLLLHNEMVSGVYKSAEQGEVENGRcITKLENMGFRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQM-----YLEHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQKL 158
                                    11        21        31|       41        51        61        71        81        91       101   |   111       121       131       141       151       
                                                         32-CSO                                                                  105   111

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: Muramoyl-pentapeptide Carboxypeptidase; domain 2 (24)

Homologous Superfamily: Trafficking protein particle complex subunit 3 (11)

Human (Homo sapiens) (2)

1a	2cfhA00	A:15-176
1b	2cfhB00	B:15-176

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (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,D (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).

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

1sz7	CRYSTAL STRUCTURE OF HUMAN BET3
2bjn	X-RAY STRUCTURE OF HUMAN TPC6
2c0j	CRYSTAL STRUCTURE OF THE BET3-TRS33 HETERODIMER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (10, 20)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 18)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File