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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CLEC-2 IN COMPLEX WITH O-GLYCOSYLATED PODOPLANIN

Authors :   M. Nagae, K. Morita-Matsumoto, M. Kato, M. Kato-Kaneko, Y. Kato, Y. Yam

Date :   20 Mar 14 (Deposition) - 22 Oct 14 (Release) - 24 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.91

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

Keywords :   C-Type Lectin Fold, Cell Surface Receptor, Podoplanin, O- Glycosylated, Extracellular Region, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nagae, K. Morita-Matsumoto, M. Kato, M. Kato-Kaneko, Y. Kato, Y. Yamaguchi
A Platform Of C-Type Lectin-Like Receptor Clec-2 For Bindin O-Glycosylated Podoplanin And Nonglycosylated Rhodocytin
Structure V. 22 1711 2014
PubMed-ID: 25458834 | Reference-DOI: 10.1016/J.STR.2014.09.009

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 1 MEMBER B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCOLD
	Expression System Strain	:	ROSETTA 2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CLEC-2, UNP RESIDUES 96-221
	Gene	:	CLEC1B, CLEC2, UNQ721/PRO1384
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	C-TYPE LECTIN-LIKE RECEPTOR 2, CLEC-2

Molecule 2 - PEPTIDE FROM PODOPLANIN
	Chains	:	C, D
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		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 (3, 6)

No.	Name	Count	Type	Full Name
1	A2G	2	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	SIA	2	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	SIA	1	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:105 , TRP A:106 , PHE A:116 , PHE A:117 , ARG A:118 , HIS A:119 , TYR A:129 , HOH A:302 , HOH A:321 , GLY B:191 , THR C:52 , GLY C:54 , HOH C:1101 , CYS D:55	BINDING SITE FOR CHAIN C OF SUGAR BOUND TO THR C 52 RESIDUES 1001 TO 1003
2	AC2	SOFTWARE	THR A:104 , ASN B:105 , TRP B:106 , PHE B:116 , PHE B:117 , ARG B:118 , HIS B:119 , TYR B:129 , HOH B:311 , THR D:52 , PRO D:53 , GLY D:54 , HOH D:1101 , HOH D:1102	BINDING SITE FOR CHAIN D OF SUGAR BOUND TO THR D 52 RESIDUES 1001 TO 1003

Asymmetric Unit

No.	Residues
1	A:102	-	A:113
2	A:130	-	A:216
3	A:195	-	A:208
4	B:102	-	B:113
5	B:130	-	B:216
6	B:195	-	B:208
7	C:55	-	D:55

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	CLC1B_HUMAN	109-217	2	A:109-217 B:109-217

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	CLC1B_HUMAN	109-217	1	A:109-217 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	CLC1B_HUMAN	109-217	1	- B:109-217

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000298527	1	ENSE00002178372	chr12:10151899-10151636	264	CLC1B_HUMAN	1-22	22	0	-	-
1.2	ENST00000298527	2	ENSE00001626056	chr12:10150979-10150881	99	CLC1B_HUMAN	22-55	34	0	-	-
1.3	ENST00000298527	3	ENSE00001677545	chr12:10149878-10149759	120	CLC1B_HUMAN	55-95	41	0	-	-
1.4a	ENST00000298527	4a	ENSE00001095413	chr12:10149599-10149445	155	CLC1B_HUMAN	95-146	52	2	A:101-146 B:101-146	46 46
1.9b	ENST00000298527	9b	ENSE00001095422	chr12:10147845-10147739	107	CLC1B_HUMAN	147-182	36	2	A:147-182 B:147-182	36 36
1.14a	ENST00000298527	14a	ENSE00001375569	chr12:10145886-10145664	223	CLC1B_HUMAN	182-229	48	2	A:182-220 B:182-220	39 39

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:120
 aligned with CLC1B_HUMAN | Q9P126 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:120
                                   110       120       130       140       150       160       170       180       190       200       210       220
          CLC1B_HUMAN   101 PCDTNWRYYGDSCYGFFRHNLTWEESKQYCTDMNATLLKIDNRNIVEYIKARTHLIRWVGLSRQKSNEVWKWEDGSVISENMFEFLEDGKGNMNCAYFHNGKMHPTFCENKHYLMCERKA 220
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh...eeeeee................hhhhhhhh........eeeee..eeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------C_TYPE_LECTIN_2  PDB: A:109-217 UniProt: 109-217                                                             --- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:101-146 UniProt: 95-146     -----------------------------------Exon 1.14a  PDB: A:182-220 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.9b  PDB: A:147-182           -------------------------------------- Transcript 1 (2)
                 3wsr A 101 PCDTNWRYYGDSCYGFFRHNLTWEESKQYCTDMNATLLKIDNRNIVEYIKARTHLIRWVGLSRQKSNEVWKWEDGSVISENMFEFLEDGKGNMNCAYFHNGKMHPTFCENKHYLMCERKA 220
                                   110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with CLC1B_HUMAN | Q9P126 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:120
                                   110       120       130       140       150       160       170       180       190       200       210       220
          CLC1B_HUMAN   101 PCDTNWRYYGDSCYGFFRHNLTWEESKQYCTDMNATLLKIDNRNIVEYIKARTHLIRWVGLSRQKSNEVWKWEDGSVISENMFEFLEDGKGNMNCAYFHNGKMHPTFCENKHYLMCERKA 220
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh...eeeeee...................hhhhh........eeeee..eeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------C_TYPE_LECTIN_2  PDB: B:109-217 UniProt: 109-217                                                             --- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: B:101-146 UniProt: 95-146     -----------------------------------Exon 1.14a  PDB: B:182-220 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.9b  PDB: B:147-182           -------------------------------------- Transcript 1 (2)
                 3wsr B 101 PCDTNWRYYGDSCYGFFRHNLTWEESKQYCTDMNATLLKIDNRNIVEYIKARTHLIRWVGLSRQKSNEVWKWEDGSVISENMFEFLEDGKGNMNCAYFHNGKMHPTFCENKHYLMCERKA 220
                                   110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with PDPN_HUMAN | Q86YL7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:10
                                    55
           PDPN_HUMAN    46 AEDDVVTPGT  55
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 3wsr C  46 AEDDVVTPGC  55
                                    55

Chain D from PDB  Type:PROTEIN  Length:11
 aligned with PDPN_HUMAN | Q86YL7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:11
                                    54 
           PDPN_HUMAN    45 GAEDDVVTPGT  55
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3wsr D  45 GAEDDVVTPGC  55
                                    54

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 3WSR)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CLC1B_HUMAN | Q9P126)

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: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:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0030220	platelet formation	The process in which platelets bud from long processes extended by megakaryocytes.
cellular component
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D (PDPN_HUMAN | Q86YL7)

molecular function
	GO:0015171	amino acid transmembrane transporter activity	Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group.
	GO:0008517	folic acid transporter activity	Enables the directed movement of folic acid (pteroylglutamic acid) into, out of or within a cell, or between cells. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
	GO:0015250	water channel activity	Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005372	water transmembrane transporter activity	Enables the directed movement of water (H2O) from one side of a membrane to the other.
biological process
	GO:0006865	amino acid transport	The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0048870	cell motility	Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0015884	folic acid transport	The directed movement of folic acid (pteroylglutamic acid) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
	GO:0048286	lung alveolus development	The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways.
	GO:0030324	lung development	The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
	GO:0001946	lymphangiogenesis	Lymph vessel formation when new vessels emerge from the proliferation of pre-existing vessels.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0051272	positive regulation of cellular component movement	Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
	GO:0006693	prostaglandin metabolic process	The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
	GO:2000045	regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0016337	single organismal cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
	GO:0006833	water transport	The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0030175	filopodium	Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
	GO:0031527	filopodium membrane	The portion of the plasma membrane surrounding a filopodium.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	GO:0031258	lamellipodium membrane	The portion of the plasma membrane surrounding a lamellipodium.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031528	microvillus membrane	The portion of the plasma membrane surrounding a microvillus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

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	3wsr
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UniProtKB/Swiss-Prot
	CLC1B_HUMAN \| Q9P126	:	2c6u 3wwk
	PDPN_HUMAN \| Q86YL7	:	4yo0

2c6u	LIGAND-FREE FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (2, 2)

SS Bonds (7, 7)

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