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Title :   CRYSTAL STRUCTURE OF VIP36 EXOPLASMIC/LUMENAL DOMAIN, METAL-FREE FORM

Authors :   T. Satoh, N. P. Cowieson, R. Kato, S. Wakatsuki

Date :   25 Jul 06 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Beta Sandwich, Carbohydrate Binding Protein, Cargo Receptor, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Satoh, N. P. Cowieson, W. Hakamata, H. Ideo, K. Fukushima, M. Kurihara, R. Kato, K. Yamashita, S. Wakatsuki
Structural Basis For Recognition Of High Mannose Type Glycoproteins By Mammalian Transport Lectin Vip36
J. Biol. Chem. V. 282 28246 2007
PubMed-ID: 17652092 | Reference-DOI: 10.1074/JBC.M703064200

Molecule 1 - VESICULAR INTEGRAL-MEMBRANE PROTEIN VIP36
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX4T-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 51-301
	Gene	:	LMAN2
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Strain	:	FAMILIARIS
	Synonym	:	LECTIN, MANNOSE-BINDING 2, VIP36

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:162 , TYR A:164 , ASN A:166 , ASP A:193 , HOH A:328 , HOH A:359	BINDING SITE FOR RESIDUE CA A 1
2	AC2	SOFTWARE	ARG A:56 , ILE A:61 , GLN A:65	BINDING SITE FOR RESIDUE CL A 2
3	AC3	SOFTWARE	ARG B:56 , ILE B:61 , GLY B:66	BINDING SITE FOR RESIDUE CL B 3
4	AC4	SOFTWARE	ARG A:209 , ASP A:210 , HIS A:211	BINDING SITE FOR RESIDUE CL A 4
5	AC5	SOFTWARE	ARG B:209 , ASP B:210 , HIS B:211	BINDING SITE FOR RESIDUE CL B 5
6	AC6	SOFTWARE	ASP B:131 , TYR B:164 , GLY B:260 , ASP B:261 , LEU B:262	BINDING SITE FOR RESIDUE GOL B 6
7	AC7	SOFTWARE	ASP A:131 , TYR A:164 , ASN A:166 , GLY A:260 , ASP A:261 , LEU A:262 , LEU B:128	BINDING SITE FOR RESIDUE GOL A 7
8	AC8	SOFTWARE	VAL A:181 , LEU A:186 , THR A:197 , LEU A:199 , ARG A:223	BINDING SITE FOR RESIDUE GOL A 8

Asymmetric Unit

No.	Residues
1	A:202	-	A:239
2	B:202	-	B:239

Asymmetric Unit

No.	Residues
1	Lys A:62	-	Pro A:63
2	Gly A:130	-	Asp A:131
3	Phe A:174	-	Pro A:175
4	Lys B:62	-	Pro B:63
5	Gly B:130	-	Asp B:131
6	Phe B:174	-	Pro B:175

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LECTIN_LIKE	PS51328	L-type lectin-like (leguminous) domain profile.	LMAN2_CANLF	52-276	1	A:52-276

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LECTIN_LIKE	PS51328	L-type lectin-like (leguminous) domain profile.	LMAN2_CANLF	52-276	1	A:52-276

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LECTIN_LIKE	PS51328	L-type lectin-like (leguminous) domain profile.	LMAN2_CANLF	52-276	0	-

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSCAFT00000026045	1	ENSCAFE00000178415	chr4:39194254-39194478	225	LMAN2_CANLF	1-67	67	2	A:52-67 B:53-67	16 15
1.2	ENSCAFT00000026045	2	ENSCAFE00000178417	chr4:39194651-39194769	119	LMAN2_CANLF	67-106	40	2	A:67-106 B:67-106	40 40
1.3	ENSCAFT00000026045	3	ENSCAFE00000178420	chr4:39207033-39207150	118	LMAN2_CANLF	107-146	40	2	A:107-146 B:107-146	40 40
1.4	ENSCAFT00000026045	4	ENSCAFE00000178423	chr4:39208399-39208478	80	LMAN2_CANLF	146-172	27	2	A:146-172 B:146-172	27 27
1.5	ENSCAFT00000026045	5	ENSCAFE00000178425	chr4:39208659-39208820	162	LMAN2_CANLF	173-226	54	2	A:173-226 B:173-226	54 54
1.6	ENSCAFT00000026045	6	ENSCAFE00000178428	chr4:39208918-39209032	115	LMAN2_CANLF	227-265	39	2	A:227-265 B:227-265	39 39
1.7	ENSCAFT00000026045	7	ENSCAFE00000178429	chr4:39212425-39212544	120	LMAN2_CANLF	265-305	41	2	A:265-301 (gaps) B:265-299 (gaps)	37 35
1.8	ENSCAFT00000026045	8	ENSCAFE00000178432	chr4:39214237-39214921	685	LMAN2_CANLF	305-357	53	0	-	-

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:245
 aligned with LMAN2_CANLF | P49256 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:250
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
          LMAN2_CANLF    52 EHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFLKS 301
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh................eeeee.eee....eeee.....eeeeeee........eeeeeeeeee.........eeeeeeee................eeeeeeee.............eeeeeeee......hhh..hhh.eeeee.........eeeeeeee..eeeeeee.......eeeeeee.ee.....eeeeeeee.....eeeeeeeeeee......-----..hhh...ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE L_LECTIN_LIKE  PDB: A:52-276 UniProt: 52-276                                                                                                                                                                                     ------------------------- PROSITE
           Transcript 1 (1) Exon 1.1        ---------------------------------------Exon 1.3  PDB: A:107-146                --------------------------Exon 1.5  PDB: A:173-226 UniProt: 173-226             Exon 1.6  PDB: A:227-265               ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.2  PDB: A:67-106 UniProt: 67-106 ---------------------------------------Exon 1.4  PDB: A:146-172   --------------------------------------------------------------------------------------------Exon 1.7  PDB: A:265-301 (gaps)       Transcript 1 (2)
                 2dup A  52 EHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHT-----IDWTKIEPSVNFLKS 301
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281     | 291       301
                                                                                                                                                                                                                                                               281   287

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with LMAN2_CANLF | P49256 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:247
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
          LMAN2_CANLF    53 HLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFL 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh................eeeee.eee....eeee.....eeeeeee........eeeeeeeeee.........eeeeeeee................eeeeeeee.............eeeeeeee......hhh..hhh.eeeee.........eeeeeeee..eeeeeee.......eeeeeee.ee.....eeeeeeee.....eeeeeeeeeee....--------.hhh...ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE L_LECTIN_LIKE  PDB: - UniProt: 52-276                                                                                                                                                                                           ----------------------- PROSITE
           Transcript 1 (1) Exon 1.1       ---------------------------------------Exon 1.3  PDB: B:107-146                --------------------------Exon 1.5  PDB: B:173-226 UniProt: 173-226             Exon 1.6  PDB: B:227-265               ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: B:67-106 UniProt: 67-106 ---------------------------------------Exon 1.4  PDB: B:146-172   --------------------------------------------------------------------------------------------Exon 1.7  PDB: B:265-299 (gaps)     Transcript 1 (2)
                 2dup B  53 HLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVE--------DWTKIEPSVNFL 299
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272      |  -     | 292       
                                                                                                                                                                                                                                                            279      288

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 2DUP)

(no "CATH Domain" information available for 2DUP)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (LMAN2_CANLF | P49256)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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: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.
cellular component
	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: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:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:130 - Asp A:131	[ RasMol ]
		Gly B:130 - Asp B:131	[ RasMol ]
		Lys A:62 - Pro A:63	[ RasMol ]
		Lys B:62 - Pro B:63	[ RasMol ]
		Phe A:174 - Pro A:175	[ RasMol ]
		Phe B:174 - Pro B:175	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	LMAN2_CANLF \| P49256
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	LMAN2_CANLF \| P49256	:	2duo 2duq 2dur 2e6v

1gv9
1r1z
2duo	THE SAME PROTEIN, CA2+-BOUND FORM
2duq	THE SAME PROTEIN, CA2+/MAN-BOUND FORM
2dur	THE SAME PROTEIN, CA2+/MAN2-BOUND FORM
2dus	THE SAME PROTEIN, CA2+/MAN3-BOUND FORM

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