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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE RABBIT IGG FC FRAGMENT

Authors :   E. Girardi, M. D. Holdom, A. M. Davies, B. J. Sutton, A. J. Beavil

Date :   27 May 08 (Deposition) - 16 Sep 08 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B

Keywords :   Immune System, Immunoglobulin C Region, Igg, Rabbit, Fc Fragment, Glycosylation, Immunoglobulins, Immunoglobulin Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Girardi, M. D. Holdom, A. M. Davies, B. J. Sutton, A. J. Beavil
The Crystal Structure Of Rabbit Igg-Fc.
Biochem. J. V. 417 77 2009
PubMed-ID: 18764781 | Reference-DOI: 10.1042/BJ20081355

Molecule 1 - IG GAMMA CHAIN C REGION
	Chains	:	A, B
	Fragment	:	FC FRAGMENT, RESIDUES 229-447
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Other Details	:	FC FRAGMENT, COMMERCIALLY AVAILABLE RABBIT IGG PURIFIED FROM SERUM (SIGMA-ALDRICH, UK)
	Synonym	:	IMMUNOGLOBULIN GAMMA HEAVY CHAIN CONSTANT REGION

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 27)

No.	Name	Count	Type	Full Name
1	AZI	2	Ligand/Ion	AZIDE ION
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	FMT	6	Ligand/Ion	FORMIC ACID
4	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
5	GOL	4	Ligand/Ion	GLYCEROL
6	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , NAG A:1446 , HOH A:2025 , HOH A:2051	BINDING SITE FOR RESIDUE NAG A1445
02	AC2	SOFTWARE	PHE A:241 , VAL A:264 , ARG A:301 , NAG A:1445 , BMA A:1447 , MAN A:1448 , HOH A:2192	BINDING SITE FOR RESIDUE NAG A1446
03	AC3	SOFTWARE	PHE A:241 , NAG A:1446 , MAN A:1448 , MAN A:1451	BINDING SITE FOR RESIDUE BMA A1447
04	AC4	SOFTWARE	ARG A:301 , NAG A:1446 , BMA A:1447 , NAG A:1449 , HOH A:2194	BINDING SITE FOR RESIDUE MAN A1448
05	AC5	SOFTWARE	PHE A:243 , THR A:260 , MAN A:1448 , GAL A:1450 , HOH A:2196 , HOH A:2197	BINDING SITE FOR RESIDUE NAG A1449
06	AC6	SOFTWARE	PRO A:244 , LYS A:246 , GLU A:258 , THR A:260 , NAG A:1449 , HOH A:2017 , HOH A:2198	BINDING SITE FOR RESIDUE GAL A1450
07	AC7	SOFTWARE	BMA A:1447 , NAG A:1452 , HOH A:2199	BINDING SITE FOR RESIDUE MAN A1451
08	AC8	SOFTWARE	MAN A:1451 , HOH A:2199	BINDING SITE FOR RESIDUE NAG A1452
09	AC9	SOFTWARE	VAL B:264 , ASP B:265 , GLN B:295 , ASN B:297 , THR B:299 , NAG B:1446 , HOH B:2183 , HOH B:2184	BINDING SITE FOR RESIDUE NAG B1445
10	BC1	SOFTWARE	PHE B:241 , VAL B:264 , ARG B:301 , NAG B:1445 , BMA B:1447 , MAN B:1448 , HOH B:2185 , HOH B:2186	BINDING SITE FOR RESIDUE NAG B1446
11	BC2	SOFTWARE	PHE B:241 , PHE B:243 , NAG B:1446 , MAN B:1448 , MAN B:1451	BINDING SITE FOR RESIDUE BMA B1447
12	BC3	SOFTWARE	PHE B:243 , NAG B:1446 , BMA B:1447 , NAG B:1449 , HOH B:2186 , HOH B:2187	BINDING SITE FOR RESIDUE MAN B1448
13	BC4	SOFTWARE	PHE B:243 , LYS B:246 , THR B:260 , MAN B:1448 , GAL B:1450 , HOH B:2188	BINDING SITE FOR RESIDUE NAG B1449
14	BC5	SOFTWARE	PHE B:243 , PRO B:244 , LYS B:246 , GLU B:258 , THR B:260 , NAG B:1449 , HOH B:2006	BINDING SITE FOR RESIDUE GAL B1450
15	BC6	SOFTWARE	BMA B:1447	BINDING SITE FOR RESIDUE MAN B1451
16	BC7	SOFTWARE	LEU A:314 , LYS A:338 , ALA A:339 , ARG A:340 , GLY A:341 , HOH A:2202	BINDING SITE FOR RESIDUE GOL A1453
17	BC8	SOFTWARE	ILE A:377 , SER A:378 , VAL A:379 , THR A:393 , HOH A:2153 , HOH A:2203 , HOH A:2204	BINDING SITE FOR RESIDUE GOL A1454
18	BC9	SOFTWARE	LEU B:314 , LYS B:338 , ARG B:340 , GLY B:341 , PRO B:343 , HOH B:2190	BINDING SITE FOR RESIDUE GOL B1452
19	CC1	SOFTWARE	PRO A:307	BINDING SITE FOR RESIDUE GOL A1455
20	CC2	SOFTWARE	GLU A:388 , ASP A:389 , ASN A:390 , HOH A:2140 , HOH A:2205	BINDING SITE FOR RESIDUE AZI A1456
21	CC3	SOFTWARE	GLU A:356 , TYR B:349 , THR B:350 , LYS B:439	BINDING SITE FOR RESIDUE AZI B1453
22	CC4	SOFTWARE	ASP A:249 , ARG A:255 , THR A:256	BINDING SITE FOR RESIDUE FMT A1457
23	CC5	SOFTWARE	ILE B:377 , SER B:378 , VAL B:379 , HOH B:2126 , HOH B:2191	BINDING SITE FOR RESIDUE FMT B1454
24	CC6	SOFTWARE	LYS A:392 , ASP B:399	BINDING SITE FOR RESIDUE FMT B1455
25	CC7	SOFTWARE	LYS A:248 , SER A:378 , GLU A:380 , SER A:426 , MET A:428 , HOH A:2206	BINDING SITE FOR RESIDUE FMT A1458
26	CC8	SOFTWARE	LYS B:248 , SER B:378 , GLU B:380 , SER B:426 , MET B:428 , HOH B:2192	BINDING SITE FOR RESIDUE FMT B1456
27	CC9	SOFTWARE	GLN B:342 , HOH B:2087	BINDING SITE FOR RESIDUE FMT B1457

Asymmetric/Biological Unit

No.	Residues
1	A:261	-	A:321
2	A:367	-	A:425
3	B:261	-	B:321
4	B:367	-	B:425

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:373	-	Pro A:374
2	Tyr B:373	-	Pro B:374

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IGHG_RABIT_002 *	T	185	A	IGHG_RABIT	---	---	A/B	A	309	A
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGHG_RABIT	299-305	2	A:423-429 B:423-429

(no "Exon" information available for 2VUO)

Asymmetric/Biological 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:215
 aligned with IGHG_RABIT | P01870 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:215
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315     
           IGHG_RABIT   106 PPPELLGGPSVFIFPPKPKDTLMISRTPEVTCVVVDVSQDDPEVQFTWYINNEQVRTARPPLREQQFNSTIRVVSTLPITHQDWLRGKEFKCKVHNKALPAPIEKTISKARGQPLEPKVYTMGPPREELSSRSVSLTCMINGFYPSDISVEWEKNGKAEDNYKTTPAVLDSDGSYFLYNKLSVPTSEWQRGDVFTCSVMHEALHNHYTQKSISRS 320
               SCOP domains d2vuoa1 A:230-341 automated matches                                                                             d2vuoa2 A:342-444 automated matches                                                                     SCOP domains
               CATH domains --------2vuoA01 A:238-337 Immunoglobulins                                                                   2vuoA02 A:338-443 Immunoglobulins                                                                         - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee......eeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vuo A 230 PPPELLGGPSVFIFPPKPKDTLMISRTPEVTCVVVDVSQDDPEVQFTWYINNEQVRTARPPLREQQFNSTIRVVSTLPIAHQDWLRGKEFKCKVHNKALPAPIEKTISKARGQPLEPKVYTMGPPREELSSRSVSLTCMINGFYPSDISVEWEKNGKAEDNYKTTPAVLDSDGSYFLYSKLSVPTSEWQRGDVFTCSVMHEALHNHYTQKSISRS 444
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with IGHG_RABIT | P01870 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:214
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    
           IGHG_RABIT   107 PPELLGGPSVFIFPPKPKDTLMISRTPEVTCVVVDVSQDDPEVQFTWYINNEQVRTARPPLREQQFNSTIRVVSTLPITHQDWLRGKEFKCKVHNKALPAPIEKTISKARGQPLEPKVYTMGPPREELSSRSVSLTCMINGFYPSDISVEWEKNGKAEDNYKTTPAVLDSDGSYFLYNKLSVPTSEWQRGDVFTCSVMHEALHNHYTQKSISRS 320
               SCOP domains d2vuob1 B:231-341 automated matches                                                                            d2vuob2 B:342-444 automated matches                                                                     SCOP domains
               CATH domains -------2vuoB01 B:238-337 Immunoglobulins                                                                   2vuoB02 B:338-443 Immunoglobulins                                                                         - CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------C1-set-2vuoB01 B:352-437                                                              ------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------C1-set-2vuoB02 B:352-437                                                              ------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------C1-set-2vuoB03 B:352-437                                                              ------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------C1-set-2vuoB04 B:352-437                                                              ------- Pfam domains (4)
         Sec.struct. author ........eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee......eeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vuo B 231 PPELLGGPSVFIFPPKPKDTLMISRTPEVTCVVVDVSQDDPEVQFTWYINNEQVRTARPPLREQQFNSTIRVVSTLPIAHQDWLRGKEFKCKVHNKALPAPIEKTISKARGQPLEPKVYTMGPPREELSSRSVSLTCMINGFYPSDISVEWEKNGKAEDNYKTTPAVLDSDGSYFLYSKLSVPTSEWQRGDVFTCSVMHEALHNHYTQKSISRS 444
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (10)

1a	d2vuoa1	A:230-341
1b	d2vuoa2	A:342-444
1c	d2vuob1	B:231-341
1d	d2vuob2	B:342-444

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Rabbit (Oryctolagus cuniculus) (5)

1a	2vuoA02	A:338-443
1b	2vuoB02	B:338-443
1c	2vuoA01	A:238-337
1d	2vuoB01	B:238-337

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Oryctolagus cuniculus (Rabbit) (1)

1a	C1-set-2vuoB01	B:352-437
1b	C1-set-2vuoB02	B:352-437
1c	C1-set-2vuoB03	B:352-437
1d	C1-set-2vuoB04	B:352-437

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IGHG_RABIT | P01870)

molecular function
	GO:0003823		antigen binding		Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987		immunoglobulin receptor binding		Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Tyr A:373 - Pro A:374	[ RasMol ]
		Tyr B:373 - Pro B:374	[ RasMol ]

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	2vuo
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 27)

Sites (27, 27)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

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