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(-) Description

Title :  CRYSTAL STRUCTURE OF IGG FC F241A MUTANT WITH NATIVE GLYCOSYLATION
 
Authors :  X. Yu, K. Baruah, D. J. Harvey, S. Vasiljevic, D. S. Alonzi, B. Song, M. K. T. A. Bowden, M. Crispin, C. N. Scanlan
Date :  07 May 13  (Deposition) - 03 Jul 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immune System, Glycan (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yu, K. Baruah, D. J. Harvey, S. Vasiljevic, D. S. Alonzi, B. Song, M. K. Higgins, T. A. Bowden, C. N. Scanlan, M. Crispin
Engineering Hydrophobic Protein-Carbohydrate Interactions To Fine-Tune Monoclonal Antibodies.
J. Am. Chem. Soc. V. 135 9723 2013
PubMed-ID: 23745692  |  Reference-DOI: 10.1021/JA4014375

(-) Compounds

Molecule 1 - IG GAMMA-1 CHAIN C REGION
    ChainsA, B
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293T
    Expression System CommonHUMAN
    Expression System Taxid9606
    Expression System VectorPHLSEC
    Expression System Vector TypePLASMID
    FragmentIMMUNOGLOBULIN GAMMA, FC, RESIDUES 101-329
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3FUL1Ligand/IonBETA-L-FUCOSE
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3FUL1Ligand/IonBETA-L-FUCOSE
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3FUL-1Ligand/IonBETA-L-FUCOSE
4MAN-1Ligand/IonALPHA-D-MANNOSE
5NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:254 , SER B:254BINDING SITE FOR RESIDUE CL A1451
2AC2SOFTWARESER A:239 , VAL A:240 , PHE A:243 , LYS A:246 , THR A:260 , VAL A:264 , ASP A:265 , GLU A:272 , GLN A:295 , TYR A:296 , ASN A:297 , ARG A:301 , LYS A:334 , HOH A:2168 , ASN B:384BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1444 THROUGH FUL A1450 BOUND TO ASN A 297

(-) SS Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003887D239EIGHG1_HUMANPolymorphism  ---A/BE356E
2UniProtVAR_003888L241MIGHG1_HUMANPolymorphism  ---A/BM358M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003887D239EIGHG1_HUMANPolymorphism  ---AE356E
2UniProtVAR_003888L241MIGHG1_HUMANPolymorphism  ---AM358M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003887D239EIGHG1_HUMANPolymorphism  ---BE356E
2UniProtVAR_003888L241MIGHG1_HUMANPolymorphism  ---BM358M

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHG1_HUMAN81-87
306-312
 
  2-
A:423-429
B:423-429
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHG1_HUMAN81-87
306-312
 
  1-
A:423-429
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGHG1_HUMAN81-87
306-312
 
  1-
-
B:423-429

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003905491ENSE00001838294chr14:106209408-106209114295IGHG1_HUMAN1-99990--
1.2ENST000003905492ENSE00001719055chr14:106208722-10620867845IGHG1_HUMAN99-114160--
1.3bENST000003905493bENSE00001776617chr14:106208559-106208230330IGHG1_HUMAN114-2241112A:237-341
B:238-341 (gaps)
105
104
1.4cENST000003905494cENSE00001837466chr14:106208132-106207675458IGHG1_HUMAN224-3301072A:341-443
B:341-445
103
105

(-) 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:207
 aligned with IGHG1_HUMAN | P01857 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:207
                                   129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       
          IGHG1_HUMAN   120 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 326
               SCOP domains d4bm7a1 A:237-341 automated matches                                                                      d4bm7a2 A:342-443 automated matches                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------E-M------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:237-341 UniProt: 114-224 [INCOMPLETE]                                                  ------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.4c  PDB: A:341-443 UniProt: 224-330 [INCOMPLETE]                                                 Transcript 1 (2)
                 4bm7 A 237 GPSVALFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with IGHG1_HUMAN | P01857 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:208
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320        
          IGHG1_HUMAN   121 PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP 328
               SCOP domains d4bm7b1 B:238-341 automate           d matches                                                          d4bm7b2 B:342-445 automated matches                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..hhhhhhh.....eeeeee-----------.eeee..eee...ee......-----.eeeeee.hhhhhhh...eeee.---------.eee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------E-M--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:238-341 (gaps) UniProt: 114-224 [INCOMPLETE]                                          -------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.4c  PDB: B:341-445 UniProt: 224-330 [INCOMPLETE]                                                   Transcript 1 (2)
                 4bm7 B 238 PSVALFPPKPKDTLMISRTPEVTCVV-----------FNWYVDGVEVHNAKTKPREEQ-----RVVSVLTVLHQDWLNGKEYKCKV---------EKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP 445
                                   247       257     |   -       277       287       | -   |   307       317     |   -     | 337       347       357       367       377       387       397       407       417       427       437        
                                                   263         275                 295   301                   323       333                                                                                                                

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BM7)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IGHG1_HUMAN | P01857)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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
        IGHG1_HUMAN | P018571aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BM7)