4GJX - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (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 CD23 LECTIN DOMAIN MUTANT D258A

Authors :   D. Yuan, B. J. Sutton, B. Dhaliwal

Date :   10 Aug 12 (Deposition) - 26 Jun 13 (Release) - 14 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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 :   Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Yuan, A. H. Keeble, R. G. Hibbert, S. Fabiane, H. J. Gould, J. M. Mcdonnell, A. J. Beavil, B. J. Sutton, B. Dhaliwal
Ca2+-Dependent Structural Changes In The B-Cell Receptor Cd23 Increase Its Affinity For Human Immunoglobulin E.
J. Biol. Chem. V. 288 21667 2013
PubMed-ID: 23775083 | Reference-DOI: 10.1074/JBC.M113.480657

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	:	UNP RESIDUES 156-298
	Gene	:	FCER2, CD23A, CLEC4J, FCE2, IGEBF
	Mutation	:	YES
	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, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 7 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 8 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:232 , GLU F:205	BINDING SITE FOR RESIDUE GOL A 301
2	AC2	SOFTWARE	VAL A:185 , ASN D:225 , LEU D:228 , ARG D:253 , SER D:254 , GLY D:256 , GLU D:257 , HOH D:413	BINDING SITE FOR RESIDUE GOL D 301

Asymmetric Unit

No.	Residues
1	A:160	-	A:288
2	A:163	-	A:174
3	A:191	-	A:282
4	A:259	-	A:273
5	B:160	-	B:288
6	B:163	-	B:174
7	B:191	-	B:282
8	B:259	-	B:273
9	C:160	-	C:288
10	C:163	-	C:174
11	C:191	-	C:282
12	C:259	-	C:273
13	D:160	-	D:288
14	D:163	-	D:174
15	D:191	-	D:282
16	D:259	-	D:273
17	E:160	-	E:288
18	E:163	-	E:174
19	E:191	-	E:282
20	E:259	-	E:273
21	F:160	-	F:288
22	F:163	-	F:174
23	F:191	-	F:282
24	F:259	-	F:273
25	G:160	-	G:288
26	G:163	-	G:174
27	G:191	-	G:282
28	G:259	-	G:273
29	H:160	-	H:288
30	H:163	-	H:174
31	H:191	-	H:282
32	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 4GJX)

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

(no "Exon" information available for 4GJX)

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:135
                                                                                                                                                                       
               SCOP domains d4gjxa_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee.eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx A 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain B from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4gjxb_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx B 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain C from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4gjxc_ C: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx C 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain D from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4gjxd_ D: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee.eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx D 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain E from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4gjxe_ E: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee.eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx E 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain F from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4gjxf_ F: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee.ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx F 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain G from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4gjxg_ G: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx G 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

Chain H from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4gjxh_ H: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhh......eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee.ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjx H 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEACVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
                                   167       177       187       197       207       217       227       237       247       257       267       277       287

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	d4gjxa_	A:
1b	d4gjxb_	B:
1c	d4gjxc_	C:
1d	d4gjxd_	D:
1e	d4gjxe_	E:
1f	d4gjxf_	F:
1g	d4gjxg_	G:
1h	d4gjxh_	H:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ 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 7	[ Jena3D ]
		Biological Unit 8	[ Jena3D ]

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	4gjx
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1t8c
1t8d
2h2r
2h2t
4ezm
4g96	WILD TYPE DERCD23
4g9a	WILD TYPE DERCD23
4gi0	DERCD23 MUTANT E249A
4gj0	DERCD23 MUTANT S252A
4gk1	DERCD23 MUTANT D270A
4gko

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (32, 32)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 8)

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