4J6K - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Biological Unit 8 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CALCIUM2+-FREE WILD-TYPE CD23 LECTIN DOMAIN (CRYSTAL FORM B)

Authors :   B. Dhaliwal, M. O. Y. Pang, B. J. Sutton

Date :   11 Feb 13 (Deposition) - 28 Aug 13 (Release) - 28 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)
Biol. Unit 6: F  (1x)
Biol. Unit 7: G  (1x)
Biol. Unit 8: H  (1x)

Keywords :   Immunoglobulin Fold Lectin, Antibody Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Dhaliwal, M. O. Pang, D. Yuan, N. Yahya, S. M. Fabiane, J. M. Mcdonnell, H. J. Gould, A. J. Beavil, B. J. Sutton
Conformational Plasticity At The Ige-Binding Site Of The B-Cell Receptor Cd23.
Mol. Immunol. V. 56 693 2013
PubMed-ID: 23933509 | Reference-DOI: 10.1016/J.MOLIMM.2013.07.005

Molecule 1 - LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SOLUBLE HEAD DOMAIN OF THE B-CELL RECEPTOR CD23 (UNP RESIDUES 156-298)
	Gene	:	CD23A, CLEC4J, FCE2, FCER2, IGEBF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BLAST-2, C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER J, FC-EPSILON- RII, IMMUNOGLOBULIN E-BINDING FACTOR, LYMPHOCYTE IGE RECEPTOR, LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR MEMBRANE-BOUND FORM, LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR SOLUBLE FORM

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E
Biological Unit 6 (1x)	:						F
Biological Unit 7 (1x)	:							G
Biological Unit 8 (1x)	:								H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 6 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 7 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 8 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:263 , SER A:265 , ARG A:267 , HOH A:305 , HOH A:326 , SER D:254 , GLN D:255 , LYS G:229	BINDING SITE FOR RESIDUE SO4 D 301
2	AC2	SOFTWARE	ARG C:263 , SER C:265 , ARG C:267 , SER F:254 , GLN F:255 , LYS H:229	BINDING SITE FOR RESIDUE SO4 F 301
3	AC3	SOFTWARE	ARG B:263 , SER B:265 , ARG B:267 , HOH B:312 , LYS D:229 , SER G:254 , GLN G:255	BINDING SITE FOR RESIDUE SO4 G 301
4	AC4	SOFTWARE	ARG E:263 , SER E:265 , ARG E:267 , LYS F:229 , SER H:254 , GLN H:255	BINDING SITE FOR RESIDUE SO4 H 301

Asymmetric Unit

No.	Residues
1	A:163	-	A:174
2	A:191	-	A:282
3	A:259	-	A:273
4	B:191	-	B:282
5	C:163	-	C:174
6	C:191	-	C:282
7	C:259	-	C:273
8	D:163	-	D:174
9	D:191	-	D:282
10	D:259	-	D:273
11	E:163	-	E:174
12	E:191	-	E:282
13	E:259	-	E:273
14	F:163	-	F:174
15	F:191	-	F:282
16	F:259	-	F:273
17	G:163	-	G:174
18	G:191	-	G:282
19	G:259	-	G:273
20	H:259	-	H:273

Asymmetric Unit

No.	Residues
1	Glu A:249	-	Pro A:250
2	Glu B:249	-	Pro B:250
3	Glu C:249	-	Pro C:250
4	Glu D:249	-	Pro D:250
5	Glu E:249	-	Pro E:250
6	Glu F:249	-	Pro F:250
7	Glu G:249	-	Pro G:250
8	Glu H:249	-	Pro H:250

(no "SAP(SNP)/Variant" information available for 4J6K)

(no "PROSITE Motif" information available for 4J6K)

(no "Exon" information available for 4J6K)

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:127
                                                                                                                                                               
               SCOP domains d4j6ka_ A: Low affinity immunoglobulin epsilon Fc receptor                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee...eee........................eeee.....eeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6k A 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATC 288
                                   168       178       188       198       208       218       231       241       251       261       271       281       
                                                                                              227|                                                         
                                                                                               231

Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4j6kb_ B: Low affinity immunoglobulin epsilon Fc receptor                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee...eee......................eeee.....eeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j6k B 162 TCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDEFIWVDGSHVDYSNWAPGEPTSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLA 286
                                   171       181       191       201       211       221     ||234       244       256       266       276       286
                                                                                           227|                  252|                               
                                                                                            231                   255

Chain C from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains d4j6kc_ C: Low affinity immunoglobulin epsilon Fc receptor                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeee........ee........................eeee.....eeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j6k C 162 TCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLAT 287
                                   171       181       191       201       211       221       231       241       251       261       271       281

Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d4j6kd_ D: Low affinity immunoglobulin epsilon Fc receptor                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6k D 156 SGFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATC 288
                                   165       175       185       195       205       215       225       235       245       255       265       275       285

Chain E from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains d4j6ke_ E: Low affinity immunoglobulin epsilon Fc receptor                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeee.....ee........................eeee.....eeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6k E 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCT 289
                                   167       177       187       197       207       217       227||     240       250       260       270       280         
                                                                                                228|                                                         
                                                                                                 232

Chain F from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains d4j6kf_ F: Low affinity immunoglobulin epsilon Fc receptor                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6k F 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLAT 287
                                   168       178       188       198       208       218       228       238       248       258       268       278

Chain G from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4j6kg_ G: Low affinity immunoglobulin epsilon Fc receptor                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6k G 157 GFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLAT 287
                                   166       176       186       196       206       216       226       236       246       256       266       276       286

Chain H from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d4j6kh_ H: Low affinity immunoglobulin epsilon Fc receptor                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhh.....eeeeeee......eee........................eeee.....eeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6k H 163 CPEKWFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDATCTP 290
                                || 174       184       194       204       214       224       234       244       254       264       274       286    
                              167|                                                                                                              283|    
                               170                                                                                                               286

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: C-type lectin domain (182)

Protein domain: Low affinity immunoglobulin epsilon Fc receptor (12)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d4j6ka_	A:
1b	d4j6kb_	B:
1c	d4j6kc_	C:
1d	d4j6kd_	D:
1e	d4j6ke_	E:
1f	d4j6kf_	F:
1g	d4j6kg_	G:
1h	d4j6kh_	H:

(no "CATH Domain" information available for 4J6K)

(no "Pfam Domain" information available for 4J6K)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:249 - Pro A:250	[ RasMol ]
		Glu B:249 - Pro B:250	[ RasMol ]
		Glu C:249 - Pro C:250	[ RasMol ]
		Glu D:249 - Pro D:250	[ RasMol ]
		Glu E:249 - Pro E:250	[ RasMol ]
		Glu F:249 - Pro F:250	[ RasMol ]
		Glu G:249 - Pro G:250	[ RasMol ]
		Glu H:249 - Pro H:250	[ RasMol ]

Biological Units
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		Biological Unit 6	[ Jena3D ]
		Biological Unit 7	[ Jena3D ]
		Biological Unit 8	[ Jena3D ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (20, 20)

Cis Peptide Bonds (8, 8)

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