3WHD - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   C-TYPE LECTIN, HUMAN MCL

Authors :   A. Furukawa, J. Kamishikiryo, D. Mori, K. Toyonaga, Y. Okabe, A. Toji, R Y. Miyake, T. Ose, S. Yamasaki, K. Maenaka

Date :   24 Aug 13 (Deposition) - 23 Oct 13 (Release) - 11 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

Chains :   Asym. Unit : A,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: A,C  (1x)

Keywords :   C-Type Lectin, Carbohydrate Recognition, Glycolipid Binding, Plasmamembrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Furukawa, J. Kamishikiryo, D. Mori, K. Toyonaga, Y. Okabe, A. Toji, R. Kanda, Y. Miyake, T. Ose, S. Yamasaki, K. Maenaka
Structural Analysis For Glycolipid Recognition By The C-Typ Lectins Mincle And Mcl
Proc. Natl. Acad. Sci. Usa V. 110 17438 2013
PubMed-ID: 24101491 | Reference-DOI: 10.1073/PNAS.1312649110

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER D
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN, UNP RESIDUES 61-215
	Gene	:	CLEC4D
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	C-TYPE LECTIN SUPERFAMILY MEMBER 8, C-TYPE LECTIN-LIKE RECEPTOR 6, CLEC-6

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:173 , ASP A:175 , ASN A:176 , ASN A:195 , ASP A:196 , HOH A:680 , HOH A:687	BINDING SITE FOR RESIDUE CA A 501
2	AC2	SOFTWARE	GLU C:173 , ASP C:175 , ASN C:195 , ASP C:196 , HOH C:624 , HOH C:693	BINDING SITE FOR RESIDUE CA C 501

Asymmetric Unit

No.	Residues
1	A:66	-	A:83
2	A:84	-	A:95
3	A:112	-	A:207
4	A:182	-	A:199
5	C:66	-	C:83
6	C:84	-	C:95
7	C:112	-	C:207
8	C:182	-	C:199

Asymmetric Unit

No.	Residues
1	Glu A:173	-	Pro A:174
2	Leu A:214	-	Asn A:215
3	Glu C:173	-	Pro C:174

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

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.	CLC4D_HUMAN	91-208	2	A:91-208 C:91-208

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.	CLC4D_HUMAN	91-208	1	A:91-208 -

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.	CLC4D_HUMAN	91-208	1	- C:91-208

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	CLC4D_HUMAN	91-208	2	A:91-208 C:91-208

(no "Exon" information available for 3WHD)

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:145
 aligned with CLC4D_HUMAN | Q8WXI8 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:155
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
          CLC4D_HUMAN    61 HAKLKCIKEKSELKSAEGSTWNCCPIDWRAFQSNCYFPLTDNKTWAESERNCSGMGAHLMTISTEAEQNFIIQFLDRRLSYFLGLRDENAKGQWRWVDQTPFNPRRVFWHKNEPDNSQGENCVVLVYNQDKWAWNDVPCNFEASRICKIPGTTLN 215
               SCOP domains d3whda_           A: automated matches                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.----------..eeeee...eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhh.......eeeeeee.......ee........................eeeeeee....eeeeeee....eeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------C_TYPE_LECTIN_2  PDB: A:91-208 UniProt: 91-208                                                                        ------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3whd A  61 HAKLKCIK----------STWNCCPIDWRAFQSNCYFPLTDNKTWAESERNCSGMGAHLMTISTEAEQNFIIQFLDRRLSYFLGLRDENAKGQWRWVDQTPFNPRRVFWHKNEPDNSQGENCVVLVYNQDKWAWNDVPCNFEASRICKIPGTTLN 215
                                   | -        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                                  68         79

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with CLC4D_HUMAN | Q8WXI8 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:156
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      
          CLC4D_HUMAN    60 HHAKLKCIKEKSELKSAEGSTWNCCPIDWRAFQSNCYFPLTDNKTWAESERNCSGMGAHLMTISTEAEQNFIIQFLDRRLSYFLGLRDENAKGQWRWVDQTPFNPRRVFWHKNEPDNSQGENCVVLVYNQDKWAWNDVPCNFEASRICKIPGTTLN 215
               SCOP domains d3whdc_ C:         automated matches                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..--------..eeeee...eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh.....eeeeeee.......ee........................eeeeeeee..eeeeeeee....eeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------C_TYPE_LECTIN_2  PDB: C:91-208 UniProt: 91-208                                                                        ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3whd C  60 MHAKLKCIKEK--------STWNCCPIDWRAFQSNCYFPLTDNKTWAESERNCSGMGAHLMTISTEAEQNFIIQFLDRRLSYFLGLRDENAKGQWRWVDQTPFNPRRVFWHKNEPDNSQGENCVVLVYNQDKWAWNDVPCNFEASRICKIPGTTLN 215
                                    69|       79        89        99       109       119       129       139       149       159       169       179       189       199       209      
                                     70       79

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: automated matches (88)

Protein domain: automated matches (88)

Human (Homo sapiens) [TaxId: 9606] (60)

1a	d3whda_	A:
1b	d3whdc_	C:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (CLC4D_HUMAN | Q8WXI8)

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:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0038094	Fc-gamma receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin G (IgG) to an Fc-gamma receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0002292	T cell differentiation involved in immune response	The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
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: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.

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	Cis Peptide Bonds
		Glu A:173 - Pro A:174	[ RasMol ]
		Glu C:173 - Pro C:174	[ RasMol ]
		Leu A:214 - Asn A:215	[ RasMol ]

Biological Units
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	3whd
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	CLC4D_HUMAN \| Q8WXI8	:	2ls8

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (8, 8)

Cis Peptide Bonds (3, 3)

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