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(-) Description

Title :  CRYSTAL STRUCTURE OF DEGLYCOSYLATED SERUM-DERIVED HUMAN IGG4 FC
 
Authors :  A. M. Davies, R. Jefferis, B. J. Sutton
Date :  12 May 14  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Immune System, Igg, Immunoglobulin, Igg1 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. M. Davies, R. Jefferis, B. J. Sutton
Crystal Structure Of Deglycosylated Human Igg4-Fc
Mol. Immunol. V. 62 46 2014
PubMed-ID: 24956411  |  Reference-DOI: 10.1016/J.MOLIMM.2014.05.015

(-) Compounds

Molecule 1 - IG GAMMA-4 CHAIN C REGION
    ChainsA, B, C, D
    FragmentFC FRAGMENT, RESIDUES 102-327
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)  CD
Biological Unit 2 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:432 , HIS B:433 , ASN B:434BINDING SITE FOR RESIDUE GOL B1444

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:261 -A:321
2A:367 -A:425
3B:261 -B:321
4B:367 -B:425
5C:261 -C:321
6C:367 -C:425
7D:261 -D:321
8D:367 -D:425

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:373 -Pro A:374
2Tyr B:373 -Pro B:374
3Tyr C:373 -Pro C:374
4Tyr D:373 -Pro D:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D2N)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHG4_HUMAN81-87
303-309
 
 
 
  4-
A:423-429
B:423-429
C:423-429
D:423-429
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHG4_HUMAN81-87
303-309
 
 
 
  2-
-
-
C:423-429
D:423-429
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHG4_HUMAN81-87
303-309
 
 
 
  2-
A:423-429
B:423-429
-
-

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003905431ENSE00001899375chr14:106092403-106092109295IGHG4_HUMAN1-99990--
1.2ENST000003905432ENSE00001619160chr14:106091716-10609168136IGHG4_HUMAN99-111130--
1.3ENST000003905433ENSE00001594509chr14:106091562-106091233330IGHG4_HUMAN111-2211114A:236-341
B:238-341
C:237-341 (gaps)
D:235-341
106
104
105
107
1.4ENST000003905434ENSE00001812352chr14:106091135-106090687449IGHG4_HUMAN221-3271074A:341-444
B:341-443
C:341-443
D:341-443
104
103
103
103

(-) Sequences/Alignments

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:209
 aligned with IGHG4_HUMAN | P01861 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:209
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315         
          IGHG4_HUMAN   116 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLS 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh......eeeeeeeee.......eeeeee..eee...eeeeeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhh...eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:236-341 UniProt: 111-221 [INCOMPLETE]                                                    ------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:341-444 UniProt: 221-327 [INCOMPLETE]                                                   Transcript 1 (2)
                 4d2n A 236 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFDSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLS 444
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435         

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with IGHG4_HUMAN | P01861 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:206
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
          IGHG4_HUMAN   118 PSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 323
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhh.....eeeeeeeee......eeeeeee..eee...eeeeeee.....eeeeeeee.hhhhhhh...eeeeeee......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:238-341 UniProt: 111-221 [INCOMPLETE]                                                  ------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.4  PDB: B:341-443 UniProt: 221-327 [INCOMPLETE]                                                  Transcript 1 (2)
                 4d2n B 238 PSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFDSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 443
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437      

Chain C from PDB  Type:PROTEIN  Length:205
 aligned with IGHG4_HUMAN | P01861 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:207
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       
          IGHG4_HUMAN   117 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 323
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee..eee...ee.....eeeeeeee.hhhhhhh...eeeeee.--...eeeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: C:237-341 (gaps) UniProt: 111-221 [INCOMPLETE]                                            ------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.4  PDB: C:341-443 UniProt: 221-327 [INCOMPLETE]                                                  Transcript 1 (2)
                 4d2n C 237 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFDSTYRVVSVLTVLHQDWLNGKEYKCKVSN--LPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 443
                                   246       256       266       276       286       296       306       316        |- |     336       346       356       366       376       386       396       406       416       426       436       
                                                                                                                  325  |                                                                                                                   
                                                                                                                     328                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:209
 aligned with IGHG4_HUMAN | P01861 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:209
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314         
          IGHG4_HUMAN   115 LGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 323
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhh.....eeeeeeeee......eeeeeee..eee...eeeeeee.....eeeeeeee.hhhhhhh...eeeeeee......eeeee..........eeeee....hhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: D:235-341 UniProt: 111-221 [INCOMPLETE]                                                     ------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------Exon 1.4  PDB: D:341-443 UniProt: 221-327 [INCOMPLETE]                                                  Transcript 1 (2)
                 4d2n D 235 LGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFDSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 443
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434         

   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  (0, 0)

(no "SCOP Domain" information available for 4D2N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D2N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D2N)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (IGHG4_HUMAN | P01861)
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.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    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.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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
        IGHG4_HUMAN | P018611adq 1bbj 2fl5 3eo1 4b53 4c54 4c55 5hvw 5lg1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4D2N)