4C9F - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF SIGN-R1 IN COMPLEX WITH SULFODEXTRAN

Authors :   N. Silva-Martin, S. G. Bartual, A. Rodriguez, E. Ramirez, P. Chacon, R. M. Anthony, C. G. Park, J. A. Hermoso

Date :   02 Oct 13 (Deposition) - 15 Oct 14 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Membrane Protein, C-Type Lectin, Innate Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Silva-Martin, S. G. Bartual, A. Rodriguez, E. Ramirez, P. Chacon, R. M. Anthony, C. G. Park, J. A. Hermoso
Structural Basis For Selective Recognition Of Endogenous And Microbial Polysaccharides By Macrophage Receptor Sign-R1
Structure V. 22 1595 2014
PubMed-ID: 25450767 | Reference-DOI: 10.1016/J.STR.2014.09.001

Molecule 1 - CD209 ANTIGEN-LIKE PROTEIN B
	Cell	:	MACROPHAGES
	Chains	:	A, B, C, D
	Fragment	:	CRD, RESIDUES 191-323
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	DC-SIGN-RELATED PROTEIN 1, DC-SIGNR1, OTB7, SIGN-R1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 20)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	GQ1	3	Ligand/Ion	4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
3	GQ2	2	Ligand/Ion	6-O-ALPHA-D-GLUCOPYRANOSYL-4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
4	GQ4	1	Ligand/Ion	ALPHA-D-GLUCOPYRANOSYL-(1->6)-ALPHA-D-GLUCOPYRANOSYL-(1->6)-ALPHA-D-GLUCOPYRANOSYL-(1->6)-4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
5	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GQ1	-1	Ligand/Ion	4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
3	GQ2	2	Ligand/Ion	6-O-ALPHA-D-GLUCOPYRANOSYL-4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
4	GQ4	-1	Ligand/Ion	ALPHA-D-GLUCOPYRANOSYL-(1->6)-ALPHA-D-GLUCOPYRANOSYL-(1->6)-ALPHA-D-GLUCOPYRANOSYL-(1->6)-4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
5	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GQ1	3	Ligand/Ion	4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
3	GQ2	-1	Ligand/Ion	6-O-ALPHA-D-GLUCOPYRANOSYL-4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
4	GQ4	1	Ligand/Ion	ALPHA-D-GLUCOPYRANOSYL-(1->6)-ALPHA-D-GLUCOPYRANOSYL-(1->6)-ALPHA-D-GLUCOPYRANOSYL-(1->6)-4-O-SULFO-ALPHA-D-GLUCOPYRANOSE
5	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:285 , ASN A:287 , GLU A:292 , ASP A:304 , GQ2 A:1324	BINDING SITE FOR RESIDUE CA A 401
02	AC2	SOFTWARE	LYS A:211 , LYS A:249 , ARG B:193 , LEU B:194 , CYS B:195 , HOH B:2006 , HOH B:2011	BINDING SITE FOR RESIDUE SO4 B1324
03	AC3	SOFTWARE	GLU B:285 , ASN B:287 , GLU B:292 , ASP B:304 , GQ2 B:1329	BINDING SITE FOR RESIDUE CA B 401
04	AC4	SOFTWARE	LEU B:203 , ASN B:205 , ASN B:234 , SER B:235 , GLU B:238 , LYS B:316 , GQ1 D:1327	BINDING SITE FOR RESIDUE SO4 B1325
05	AC5	SOFTWARE	SER B:235 , ASP B:236 , GLU B:237 , SO4 B:1327	BINDING SITE FOR RESIDUE SO4 B1326
06	AC6	SOFTWARE	ARG A:193 , LEU A:194 , CYS A:195 , PHE A:201 , HOH A:2006 , LYS B:211 , LYS B:249	BINDING SITE FOR RESIDUE SO4 A1323
07	AC7	SOFTWARE	GLU C:285 , ASN C:287 , GLU C:292 , ASP C:304 , GQ4 C:1325	BINDING SITE FOR RESIDUE CA C 401
08	AC8	SOFTWARE	SER C:235 , ASP C:236 , GLU C:237 , ARG C:276 , HOH C:2038 , HOH C:2039	BINDING SITE FOR RESIDUE SO4 C1323
09	AC9	SOFTWARE	LYS C:211 , LYS C:249 , HOH C:2004 , ARG D:193 , LEU D:194 , CYS D:195 , HOH D:2007	BINDING SITE FOR RESIDUE SO4 D1324
10	BC1	SOFTWARE	GLU D:285 , ASN D:287 , GLU D:292 , ASP D:304	BINDING SITE FOR RESIDUE CA D 401
11	BC2	SOFTWARE	SER B:235 , ASP B:236 , ARG B:276 , SO4 B:1326 , HOH B:2022 , HOH B:2044	BINDING SITE FOR RESIDUE SO4 B1327
12	BC3	SOFTWARE	TRP A:199 , VAL A:226 , TRP C:199 , VAL C:226 , HOH C:2036	BINDING SITE FOR RESIDUE SO4 C1324
13	BC4	SOFTWARE	PHE B:208 , SER B:210 , LYS B:211 , SER B:212	BINDING SITE FOR RESIDUE SO4 B1328
14	BC5	SOFTWARE	LYS B:260 , GLN C:213 , LYS C:249 , PRO C:251 , GLU C:285 , ASN C:287 , ASN C:288 , GLU C:292 , GLU C:296 , SER C:305 , LEU C:309 , LYS C:311 , CA C:401 , SO4 C:1326 , HOH C:2040 , THR D:323	BINDING SITE FOR RESIDUE GQ4 C1325
15	BC6	SOFTWARE	GLU A:285 , ASN A:287 , ASN A:288 , GLU A:292 , GLU A:296 , ASP A:304 , SER A:305 , LEU A:309 , LYS A:311 , CA A:401	BINDING SITE FOR RESIDUE GQ2 A1324
16	BC7	SOFTWARE	PRO B:251 , GLU B:285 , ASN B:287 , ASN B:288 , GLU B:296 , ASN B:303 , SER B:305 , LYS B:311 , CA B:401	BINDING SITE FOR RESIDUE GQ2 B1329
17	BC8	SOFTWARE	ASN D:234 , SER D:235 , ASP D:236 , GLU D:237 , ARG D:276	BINDING SITE FOR RESIDUE GQ1 D1325
18	BC9	SOFTWARE	LYS D:279 , ASN D:287 , ASN D:288 , ILE D:289	BINDING SITE FOR RESIDUE GQ1 D1326
19	CC1	SOFTWARE	LEU B:259 , LYS B:260 , GQ4 C:1325	BINDING SITE FOR RESIDUE SO4 C1326
20	CC2	SOFTWARE	ASN B:234 , SO4 B:1325 , ASN D:205 , ASN D:234 , SER D:235 , GLU D:238 , LYS D:316 , HOH D:2008 , HOH D:2009	BINDING SITE FOR RESIDUE GQ1 D1327

Asymmetric Unit

No.	Residues
1	A:192	-	A:322
2	A:195	-	A:206
3	A:223	-	A:315
4	A:294	-	A:307
5	B:192	-	B:322
6	B:195	-	B:206
7	B:223	-	B:315
8	B:294	-	B:307
9	C:192	-	C:322
10	C:195	-	C:206
11	C:223	-	C:315
12	C:294	-	C:307
13	D:192	-	D:322
14	D:195	-	D:206
15	D:223	-	D:315
16	D:294	-	D:307

Asymmetric Unit

No.	Residues
1	Glu A:285	-	Pro A:286
2	Glu B:285	-	Pro B:286
3	Glu C:285	-	Pro C:286
4	Glu D:285	-	Pro D:286

(no "SAP(SNP)/Variant" information available for 4C9F)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	C209B_MOUSE	202-316	4	A:202-316 B:202-316 C:202-316 D:202-316
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	C209B_MOUSE	294-315	4	A:294-315 B:294-315 C:294-315 D:294-315

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	C209B_MOUSE	202-316	2	A:202-316 B:202-316 - -
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	C209B_MOUSE	294-315	2	A:294-315 B:294-315 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	C209B_MOUSE	202-316	2	- - C:202-316 D:202-316
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	C209B_MOUSE	294-315	2	- - C:294-315 D:294-315

(no "Exon" information available for 4C9F)

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:132
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:132
                                   200       210       220       230       240       250       260       270       280       290       300       310       320  
          C209B_MOUSE   191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.eeeeee........ee......hhhhhhh.............eeeee..eeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------C_TYPE_LECTIN_2  PDB: A:202-316 UniProt: 202-316                                                                   ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c9f A 191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
                                   200       210       220       230       240       250       260       270       280       290       300       310       320

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:133
                                   200       210       220       230       240       250       260       270       280       290       300       310       320   
          C209B_MOUSE   191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPCT 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.eeeeeeeeee..eeee......hhhhhhh.............eeeee..eeeee......eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------C_TYPE_LECTIN_2  PDB: B:202-316 UniProt: 202-316                                                                   ------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       -------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c9f B 191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPCT 323
                                   200       210       220       230       240       250       260       270       280       290       300       310       320

Chain C from PDB  Type:PROTEIN  Length:132
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:132
                                   200       210       220       230       240       250       260       270       280       290       300       310       320  
          C209B_MOUSE   191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.eeeeeeeeee..eeee......hhhhhhh.............eeeee..eeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------C_TYPE_LECTIN_2  PDB: C:202-316 UniProt: 202-316                                                                   ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c9f C 191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
                                   200       210       220       230       240       250       260       270       280       290       300       310       320

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:134
                                   199       209       219       229       239       249       259       269       279       289       299       309       319    
          C209B_MOUSE   190 RLCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPCT 323
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..eeeee....eehhhhhhhhhhh..ee....hhhhhhhhhhhhhh...eeeeee........ee......hhhhhhh.............eeeee..eeeee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------C_TYPE_LECTIN_2  PDB: D:202-316 UniProt: 202-316                                                                   ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       -------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c9f D 190 KLCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPCT 323
                                   199       209       219       229       239       249       259       269       279       289       299       309       319

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 4C9F)

(no "CATH Domain" information available for 4C9F)

(no "Pfam Domain" information available for 4C9F)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (C209B_MOUSE | Q8CJ91)

molecular function
	GO:0001872	(1->3)-beta-D-glucan binding	Interacting selectively and non-covalently with (1->3)-beta-D-glucans.
	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:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
biological process
	GO:0016045	detection of bacterium	The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
	GO:0001879	detection of yeast	The series of events in which a stimulus from a yeast is received and converted into a molecular signal.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050766	positive regulation of phagocytosis	Any process that activates or increases the frequency, rate or extent of phagocytosis.
	GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
cellular component
	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: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.

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	Cis Peptide Bonds
		Glu A:285 - Pro A:286	[ RasMol ]
		Glu B:285 - Pro B:286	[ RasMol ]
		Glu C:285 - Pro C:286	[ RasMol ]
		Glu D:285 - Pro D:286	[ RasMol ]

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	4c9f
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	C209B_MOUSE \| Q8CJ91
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	C209B_MOUSE \| Q8CJ91	:	3zhg 4caj

(no "Related Entries Specified in the PDB File" available for 4C9F)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 20)

Sites (20, 20)

SS Bonds (16, 16)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (14, 14)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File