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(-) Description

Title :  NON-FCRN BINDING FC FRAGMENT OF RAT IGG2A
 
Authors :  W. L. Martin, A. P. West Jr. , L. Gan, P. J. Bjorkman
Date :  31 Jan 01  (Deposition) - 14 Feb 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Igg, Fc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. L. Martin, A. P. West Jr. , L. Gan, P. J. Bjorkman
Crystal Structure At 2. 8 A Of An Fcrn/Heterodimeric Fc Complex: Mechanism Of Ph-Dependent Binding.
Mol. Cell V. 7 867 2001
PubMed-ID: 11336709  |  Reference-DOI: 10.1016/S1097-2765(01)00230-1

(-) Compounds

Molecule 1 - IG GAMMA-2A CHAIN C REGION
    Chains: A, B
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Organ: OVARY
    Expression System Plasmid: PBJ-5GS
    Expression System Strain: CHO-K1
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Fragment: FC FRAGMENT
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: IGG2A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3FUL1Ligand/IonBETA-L-FUCOSE
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREFUL A:102 , NAG A:103 , VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , THR A:299BINDING SITE FOR RESIDUE NAG A 101
02AC2SOFTWARENAG A:101 , NAG A:103BINDING SITE FOR RESIDUE FUL A 102
03AC3SOFTWARENAG A:101 , FUL A:102 , BMA A:104 , MAN A:105 , PHE A:241 , VAL A:264 , ARG A:301BINDING SITE FOR RESIDUE NAG A 103
04AC4SOFTWARENAG A:103 , MAN A:105 , MAN A:108 , PHE A:243BINDING SITE FOR RESIDUE BMA A 104
05AC5SOFTWARENAG A:103 , BMA A:104 , NAG A:106 , PHE A:243BINDING SITE FOR RESIDUE MAN A 105
06AC6SOFTWAREMAN A:105 , LYS A:246BINDING SITE FOR RESIDUE NAG A 106
07AC7SOFTWAREBMA A:104 , NAG A:109 , NAG B:201 , FUC B:202 , NAG B:203BINDING SITE FOR RESIDUE MAN A 108
08AC8SOFTWAREMAN A:108 , FUC B:202BINDING SITE FOR RESIDUE NAG A 109
09AC9SOFTWAREMAN A:108 , FUC B:202 , NAG B:203 , VAL B:264 , ASP B:265 , GLN B:295 , ASN B:297 , THR B:299BINDING SITE FOR RESIDUE NAG B 201
10BC1SOFTWAREMAN A:108 , NAG A:109 , NAG B:201 , NAG B:203BINDING SITE FOR RESIDUE FUC B 202
11BC2SOFTWAREMAN A:108 , NAG B:201 , FUC B:202 , BMA B:204 , MAN B:205 , PHE B:241 , VAL B:262 , VAL B:264 , ARG B:301BINDING SITE FOR RESIDUE NAG B 203
12BC3SOFTWARENAG B:203 , MAN B:205 , MAN B:208 , PHE B:243BINDING SITE FOR RESIDUE BMA B 204
13BC4SOFTWARENAG B:203 , BMA B:204 , NAG B:206 , PHE B:243BINDING SITE FOR RESIDUE MAN B 205
14BC5SOFTWAREMAN B:205 , PHE B:243 , LYS B:246 , VAL B:262BINDING SITE FOR RESIDUE NAG B 206
15BC6SOFTWAREBMA B:204 , NAG B:209BINDING SITE FOR RESIDUE MAN B 208
16BC7SOFTWAREMAN B:208BINDING SITE FOR RESIDUE NAG B 209

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:261 -A:321
2A:367 -A:425
3B:261 -B:321
4B:367 -B:425

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:373 -Pro A:374
2Tyr B:373 -Pro B:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I1C)

(-) Exons   (0, 0)

(no "Exon" information available for 1I1C)

(-) Sequences/Alignments

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:205
 aligned with IGG2A_RAT | P20760 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:205
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
            IGG2A_RAT   114 SVFIFPPKTKDVLTITLTPKVTCVVVDISQNDPEVRFSWFIDDVEVHTAQTHAPEKQSNSTLRSVSELPIVHRDWLNGKTFKCKVNSGAFPAPIEKSISKPEGTPRGPQVYTMAPPKEEMTQSQVSITCMVKGFYPPDIYTEWKMNGQPQENYKNTPPTMDTDGSYFLYSKLNVKKETWQQGNTFTCSVLHEGLHNHHTEKSLSH 318
               SCOP domains d1i1ca1 A:239-341 Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma                        d1i1ca2 A:342-443 Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma                        SCOP domains
               CATH domains 1i1cA01 A:239-337 Immunoglobulins                                                                  1i1cA02 A:338-443 Immunoglobulins                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhh......eeeeeeeee.......eeeeee...ee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i1c A 239 SVFIFPPKTKDVLGGGLTPKVTCVVVDISQNDPEVRFSWFIDDVEVHTAQTHAPEKQSNSTLRSVSELPIVERDWLNGKTFKCKVNSGAFPAPIEKSISKPEGTPRGPQVYTMAPPKEEMTQSQVSITCMVKGFYPPDIYTEWKMNGQPQENYKNTPPTMDTDGSYFLYSKLNVKKETWQQGNTFTCSVLHEGLENEHTEKSLSH 443
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with IGG2A_RAT | P20760 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:205
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
            IGG2A_RAT   114 SVFIFPPKTKDVLTITLTPKVTCVVVDISQNDPEVRFSWFIDDVEVHTAQTHAPEKQSNSTLRSVSELPIVHRDWLNGKTFKCKVNSGAFPAPIEKSISKPEGTPRGPQVYTMAPPKEEMTQSQVSITCMVKGFYPPDIYTEWKMNGQPQENYKNTPPTMDTDGSYFLYSKLNVKKETWQQGNTFTCSVLHEGLHNHHTEKSLSH 318
               SCOP domains d1i1cb1 B:239-341 Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma                        d1i1cb2 B:342-443 Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma                        SCOP domains
               CATH domains 1i1cB01 B:239-337 Immunoglobulins                                                                  1i1cB02 B:338-443 Immunoglobulins                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhh......eeeeeeeee.......eeeeee...ee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i1c B 239 SVFIFPPKTKDVLGGGLTPKVTCVVVDISQNDPEVRFSWFIDDVEVHTAQTHAPEKQSNSTLRSVSELPIVERDWLNGKTFKCKVNSGAFPAPIEKSISKPEGTPRGPQVYTMAPPKEEMTQSQVSITCMVKGFYPPDIYTEWKMNGQPQENYKNTPPTMDTDGSYFLYSKLNVKKETWQQGNTFTCSVLHEGLENEHTEKSLSH 443
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I1C)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IGG2A_RAT | P20760)
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.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IGG2A_RAT | P20760: 1fn4 1i1a 4uao

(-) Related Entries Specified in the PDB File

1fc1 HUMAN FC FRAGMENT OF IGG
1i1a NEONATAL FC RECEPTOR COMPLEXED WITH A HETERODIMERIC FC