2DUR - JenaLib

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Title :   CRYSTAL STRUCTURE OF VIP36 EXOPLASMIC/LUMENAL DOMAIN, CA2+/MAN2-BOUND 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 :   1.65

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 (4, 16)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	8	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE

Biological Unit 1 (2, 4)

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
4	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE

Biological Unit 2 (1, 2)

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
4	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MAN A:14 , ASP A:131 , ASN A:166 , HIS A:190 , GLY A:260 , ASP A:261 , LEU A:262 , HOH A:362 , HOH A:472 , LYS B:125 , LEU B:128	BINDING SITE FOR RESIDUE MAN A 13
02	AC2	SOFTWARE	MAN A:13 , SER A:96 , GLY A:260 , ASP A:261 , HOH A:406 , HOH A:441 , HOH A:519 , THR B:123 , LYS B:125	BINDING SITE FOR RESIDUE MAN A 14
03	AC3	SOFTWARE	LYS A:125 , LEU A:128 , MAN B:16 , ASP B:131 , ASN B:166 , HIS B:190 , GLY B:260 , ASP B:261 , LEU B:262 , HOH B:341 , HOH B:445	BINDING SITE FOR RESIDUE MAN B 15
04	AC4	SOFTWARE	LYS A:125 , MAN B:15 , SER B:96 , GLY B:260 , ASP B:261 , HOH B:409	BINDING SITE FOR RESIDUE MAN B 16
05	AC5	SOFTWARE	ASP A:162 , TYR A:164 , ASN A:166 , ASP A:193 , HOH A:313 , HOH A:332	BINDING SITE FOR RESIDUE CA A 1
06	AC6	SOFTWARE	ASP B:162 , TYR B:164 , ASN B:166 , ASP B:193 , HOH B:323 , HOH B:324	BINDING SITE FOR RESIDUE CA B 2
07	AC7	SOFTWARE	ARG A:56 , LEU A:60 , ILE A:61 , TYR A:64 , GLN A:65	BINDING SITE FOR RESIDUE CL A 3
08	AC8	SOFTWARE	ARG B:56 , GLY B:66	BINDING SITE FOR RESIDUE CL B 4
09	AC9	SOFTWARE	ARG A:209 , ASP A:210	BINDING SITE FOR RESIDUE CL A 5
10	BC1	SOFTWARE	ARG B:209 , ASP B:210	BINDING SITE FOR RESIDUE CL B 6
11	BC2	SOFTWARE	GLY B:68 , SER B:70 , MET B:72	BINDING SITE FOR RESIDUE CL B 7
12	BC3	SOFTWARE	ARG A:95 , ARG B:95 , HOH B:326	BINDING SITE FOR RESIDUE CL A 8
13	BC4	SOFTWARE	THR A:228 , LEU A:230 , HOH A:366 , HOH A:419	BINDING SITE FOR RESIDUE CL A 9
14	BC5	SOFTWARE	ASN A:166 , LYS B:126	BINDING SITE FOR RESIDUE CL A 10
15	BC6	SOFTWARE	MET A:180 , VAL A:181 , THR A:197 , ARG A:223 , HOH A:497 , HOH A:534	BINDING SITE FOR RESIDUE GOL A 11
16	BC7	SOFTWARE	ARG A:139 , TYR A:251 , HOH A:317 , HOH A:340 , HOH A:359 , HOH A:523	BINDING SITE FOR RESIDUE GOL A 12

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 2DUR)

Asymmetric Unit (1, 2)

	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	2	A:52-276 B: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 (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	- B:52-276

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:51-67 B:51-67	17 17
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 B:265-300	37 36
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:251
 aligned with LMAN2_CANLF | P49256 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:251
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
          LMAN2_CANLF    51 SEHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFLKS 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......hhhhh..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 [INCOMPLETE] Transcript 1 (2)
                 2dur A  51 SEHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFLKS 301
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with LMAN2_CANLF | P49256 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:250
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
          LMAN2_CANLF    51 SEHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFLK 300
               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......hhhhh..hhh...ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -L_LECTIN_LIKE  PDB: B:52-276 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:265-300             Transcript 1 (2)
                 2dur B  51 SEHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETTERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTVMTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFLK 300
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

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 2DUR)

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

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

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.

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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 ]

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

1gv9
1r1z
2duo	THE SAME PROTEIN, CA2+-BOUND FORM
2dup	THE SAME PROTEIN, METAL-FREE FORM
2duq	THE SAME PROTEIN, CA2+/MAN-BOUND FORM
2dus	THE SAME PROTEIN, CA2+/MAN3-BOUND FORM

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (2, 2)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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