4AK8 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF F241L MUTANT OF LANGERIN CARBOHYDRATE RECOGNITION DOMAIN.

Authors :   E. Chabrol, M. Thepaut, C. Dezutter-Dambuyant, C. Vives, J. Marcoux, R J. Valadeau-Guilemond, P. Vachette, D. Durand, F. Fieschi

Date :   22 Feb 12 (Deposition) - 03 Apr 13 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Sugar Binding Protein, Langerhans Cells, Dc-Sign, Hiv, Birbeck Granules (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Chabrol, M. Thepaut, C. Dezutter-Dambuyant, C. Vives, J. Marcoux, R. Kahn, J. Valladeau-Guilemond, P. Vachette, D. Durand, F. Fieschi
Alteration Of The Langerin Oligomerization State Affects Birbeck Granule Formation.
Biophys. J. V. 108 666 2015
PubMed-ID: 25650933 | Reference-DOI: 10.1016/J.BPJ.2014.10.075

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER K
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 188-328
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LANGERIN, CD_ANTIGEN=CD207

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

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

Biological Unit 1 (0, 0)

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

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:285 , ASN A:287 , GLU A:293 , ASN A:307 , ASP A:308 , HOH A:2151 , HOH A:2180	BINDING SITE FOR RESIDUE CA A1326
2	AC2	SOFTWARE	TYR A:208 , SER A:210 , LEU A:211 , ILE A:212	BINDING SITE FOR RESIDUE MG A1327
3	AC3	SOFTWARE	GLU B:285 , ASN B:287 , GLU B:293 , ASN B:307 , ASP B:308 , HOH B:2137 , HOH B:2161	BINDING SITE FOR RESIDUE CA B1326
4	AC4	SOFTWARE	TYR B:208 , SER B:210 , LEU B:211 , ILE B:212	BINDING SITE FOR RESIDUE MG B1327
5	AC5	SOFTWARE	GLU C:285 , ASN C:287 , GLU C:293 , ASN C:307 , ASP C:308 , HOH C:2123 , HOH C:2148	BINDING SITE FOR RESIDUE CA C1326
6	AC6	SOFTWARE	GLN C:197 , TYR C:208 , SER C:210 , LEU C:211 , ILE C:212	BINDING SITE FOR RESIDUE MG C1327
7	AC7	SOFTWARE	GLU D:236 , ARG D:279	BINDING SITE FOR RESIDUE CL D1329
8	AC8	SOFTWARE	GLU D:285 , ASN D:287 , GLU D:293 , ASN D:307 , ASP D:308 , HOH D:2126 , HOH D:2160	BINDING SITE FOR RESIDUE CA D1330
9	AC9	SOFTWARE	TYR D:208 , LEU D:211 , ILE D:212 , HOH D:2199	BINDING SITE FOR RESIDUE MG D1331

Asymmetric Unit

No.	Residues
1	A:223	-	A:319
2	A:295	-	A:311
3	B:223	-	B:319
4	B:295	-	B:311
5	C:223	-	C:319
6	C:295	-	C:311
7	D:223	-	D:319
8	D:295	-	D:311

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

Asymmetric Unit (5, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054782	P	213	S	CLC4K_HUMAN	Polymorphism	17006436	A/B/C/D	P	213	S
2	UniProt	VAR_063828	W	264	R	CLC4K_HUMAN	Disease (BIRGD)	200837270	A/B/C/D	W	264	R
3	UniProt	VAR_054783	V	278	A	CLC4K_HUMAN	Polymorphism	741326	A/B/C/D	A	278	A
4	UniProt	VAR_054784	N	288	D	CLC4K_HUMAN	Polymorphism	13383830	A/B/C/D	N	288	D
5	UniProt	VAR_059448	A	300	P	CLC4K_HUMAN	Polymorphism	2080391	A/B/C/D	A	300	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (5, 40)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054782	P	213	S	CLC4K_HUMAN	Polymorphism	17006436	A/B/C/D	P	213	S
2	UniProt	VAR_063828	W	264	R	CLC4K_HUMAN	Disease (BIRGD)	200837270	A/B/C/D	W	264	R
3	UniProt	VAR_054783	V	278	A	CLC4K_HUMAN	Polymorphism	741326	A/B/C/D	A	278	A
4	UniProt	VAR_054784	N	288	D	CLC4K_HUMAN	Polymorphism	13383830	A/B/C/D	N	288	D
5	UniProt	VAR_059448	A	300	P	CLC4K_HUMAN	Polymorphism	2080391	A/B/C/D	A	300	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	CLC4K_HUMAN	202-320	4	A:202-320 B:202-320 C:202-320 D:202-320
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	CLC4K_HUMAN	295-319	4	A:295-319 B:295-319 C:295-319 D:295-319

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	CLC4K_HUMAN	202-320	8	A:202-320 B:202-320 C:202-320 D:202-320
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	CLC4K_HUMAN	295-319	8	A:295-319 B:295-319 C:295-319 D:295-319

(no "Exon" information available for 4AK8)

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:130
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:130
                                   205       215       225       235       245       255       265       275       285       295       305       315       325
          CLC4K_HUMAN   196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
               SCOP domains d4ak8a_ A: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhh.........hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------S--------------------------------------------------R-------------A---------D-----------P------------------------- SAPs(SNPs)
                PROSITE (1) ------C_TYPE_LECTIN_2  PDB: A:202-320 UniProt: 202-320                                                                       ----- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ak8 A 196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQELLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
                                   205       215       225       235       245       255       265       275       285       295       305       315       325

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:128
                                   207       217       227       237       247       257       267       277       287       297       307       317        
          CLC4K_HUMAN   198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
               SCOP domains d4ak8b_ B: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhh.........hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------S--------------------------------------------------R-------------A---------D-----------P------------------------- SAPs(SNPs)
                PROSITE (1) ----C_TYPE_LECTIN_2  PDB: B:202-320 UniProt: 202-320                                                                       ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ak8 B 198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQELLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
                                   207       217       227       237       247       257       267       277       287       297       307       317

Chain C from PDB  Type:PROTEIN  Length:130
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:130
                                   205       215       225       235       245       255       265       275       285       295       305       315       325
          CLC4K_HUMAN   196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
               SCOP domains d4ak8c_ C: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhh.........hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------S--------------------------------------------------R-------------A---------D-----------P------------------------- SAPs(SNPs)
                PROSITE (1) ------C_TYPE_LECTIN_2  PDB: C:202-320 UniProt: 202-320                                                                       ----- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ak8 C 196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQELLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
                                   205       215       225       235       245       255       265       275       285       295       305       315       325

Chain D from PDB  Type:PROTEIN  Length:133
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:133
                                   205       215       225       235       245       255       265       275       285       295       305       315       325   
          CLC4K_HUMAN   196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVPSEP 328
               SCOP domains d4ak8d_ D: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhh.........hhhhh..eeee.......eeee......eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -----------------S--------------------------------------------------R-------------A---------D-----------P---------------------------- SAPs(SNPs)
                PROSITE (1) ------C_TYPE_LECTIN_2  PDB: D:202-320 UniProt: 202-320                                                                       -------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          --------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ak8 D 196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQELLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVPSEP 328
                                   205       215       225       235       245       255       265       275       285       295       305       315       325

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	d4ak8a_	A:
1b	d4ak8b_	B:
1c	d4ak8c_	C:
1d	d4ak8d_	D:

(no "CATH Domain" information available for 4AK8)

(no "Pfam Domain" information available for 4AK8)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CLC4K_HUMAN | Q9UJ71)

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: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.
biological process
	GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	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.

Asymmetric Unit
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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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	4ak8
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(no "Related Entries Specified in the PDB File" available for 4AK8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 20)

PROSITE Motifs (2, 8)

Exons (0, 0)

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