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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ISOLATED IGG4 CH3 DOMAIN
 
Authors :  A. M. Davies, T. Rispens, T. H. Den Bleker, J. M. Mcdonnell, H. J. Gould, R. C. Aalberse, B. J. Sutton
Date :  02 Aug 12  (Deposition) - 05 Dec 12  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immune System, Antibody, Immunoglobulin, Fab Arm Exchange, Igg1 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. M. Davies, T. Rispens, T. H. Den Bleker, J. M. Mcdonnell, H. J. Gould R. C. Aalberse, B. J. Sutton
Crystal Structure Of The Human Igg4 C(H)3 Dimer Reveals The Role Of Arg409 In The Mechanism Of Fab-Arm Exchange.
Mol. Immunol. V. 54 1 2012
PubMed-ID: 23164605  |  Reference-DOI: 10.1016/J.MOLIMM.2012.10.029

(-) Compounds

Molecule 1 - IG GAMMA-4 CHAIN C REGION
    ChainsA, B
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293F
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentCH3 DOMAIN, RESIDUES 222-327
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsN TERMINAL GLUTAMINE 342 IS MODIFIED TO PYROGLUTAMATE
    SynonymHUMAN IGG4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:378 , GLU A:380 , SER A:426 , MET A:428 , PEG A:1451BINDING SITE FOR RESIDUE EDO A1447
02AC2SOFTWAREGLN A:347 , VAL A:348 , LYS A:439 , HOH A:2006 , HOH A:2110BINDING SITE FOR RESIDUE EDO A1448
03AC3SOFTWAREMET A:428 , HOH A:2109BINDING SITE FOR RESIDUE EDO A1449
04AC4SOFTWAREASN A:361 , SER A:400 , ASP A:401 , ASP A:413 , LYS A:414 , SER A:415 , HOH A:2117BINDING SITE FOR RESIDUE PEG A1450
05AC5SOFTWAREGLU A:382 , SER A:426 , TYR A:436 , GLN A:438 , EDO A:1447 , HOH A:2118 , GLU B:382 , GLY B:385 , GLN B:386BINDING SITE FOR RESIDUE PEG A1451
06AC6SOFTWAREASN A:434 , HOH A:2107 , GLU B:419 , ASN B:421BINDING SITE FOR RESIDUE TRS A1452
07AC7SOFTWAREGLN A:438 , GLU B:382 , SER B:383 , ASN B:384 , GLY B:385 , SER B:424 , HOH B:2040BINDING SITE FOR RESIDUE ACT B1445
08AC8SOFTWAREALA B:378 , GLU B:380 , SER B:426 , MET B:428BINDING SITE FOR RESIDUE EDO B1446
09AC9SOFTWAREILE B:377 , ALA B:378 , MET B:428 , HOH B:2031 , HOH B:2077BINDING SITE FOR RESIDUE EDO B1447
10BC1SOFTWAREHOH A:2025 , HOH A:2034 , GLU B:345 , PRO B:346 , GLN B:347 , VAL B:348 , TYR B:349 , LEU B:432 , THR B:437 , LYS B:439BINDING SITE FOR RESIDUE PEG B1448
11BC2SOFTWAREHOH A:2098 , ASN B:434BINDING SITE FOR RESIDUE PEG A1456

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:367 -A:425
2B:367 -B:425

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 4B53)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003905431ENSE00001899375chr14:106092403-106092109295IGHG4_HUMAN1-99990--
1.2ENST000003905432ENSE00001619160chr14:106091716-10609168136IGHG4_HUMAN99-111130--
1.3ENST000003905433ENSE00001594509chr14:106091562-106091233330IGHG4_HUMAN111-2211110--
1.4ENST000003905434ENSE00001812352chr14:106091135-106090687449IGHG4_HUMAN221-3271072A:342-445
B:342-443
104
102

(-) 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:104
 aligned with IGHG4_HUMAN | P01861 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:104
                                   231       241       251       261       271       281       291       301       311       321    
          IGHG4_HUMAN   222 QPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSL 325
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
               Transcript 1 Exon 1.4  PDB: A:342-445 UniProt: 221-327 [INCOMPLETE]                                                   Transcript 1
                 4b53 A 342 xPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSL 445
                            |      351       361       371       381       391       401       411       421       431       441    
                            |                                                                                                       
                          342-PCA                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with IGHG4_HUMAN | P01861 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:102
                                   231       241       251       261       271       281       291       301       311       321  
          IGHG4_HUMAN   222 QPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 323
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------IG_MHC -------------- PROSITE
               Transcript 1 Exon 1.4  PDB: B:342-443 UniProt: 221-327 [INCOMPLETE]                                                 Transcript 1
                 4b53 B 342 xPREPQVYTLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSL 443
                            |      351       361       371       381       391       401       411       421       431       441  
                          342-PCA                                                                                                 

   Legend:   → Mismatch (orange background)
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  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 4B53)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B53)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B53)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 4c54 4c55 4d2n 5hvw 5lg1

(-) Related Entries Specified in the PDB File

1adq CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC
4b51 CRYSTAL STRUCTURE OF THE ISOLATED IGG4 CH3 DOMAIN