BMRB Entry 53464

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53464

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Title:
Methyl group assignment of a non-glycosylated IgG1 Fc fragment
Deposition date:
2025-12-02
Original release date:
2025-12-12
Authors:
Vibert, Beatrice; Frances, Oriane; Boisbouvier, Jerome
Citation:

Citation: Vibert, Beatrice; Nguyen, Sarah; Henot, Faustine; Doyen, Camille; Hernandez-Alba, Oscar; Cianferani, Sarah; Clavier, Severine; Frances, Oriane; Boisbouvier, Jerome. "Toward Site-Specific Characterization of Structural Perturbations on Glycosylated Fc Using NMR at Natural Abundance"  J. Biomol. NMR ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 245 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: cell free synthesis   Host organism: Escherichia coli   Vector: pIVEX 2.3d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MDKTHTCPPCPAPELLGGPS VFLFPPKPKDTLMISRTPEV TCVVVDVSHEDPEVKFNWYV DGVEVHNAKTKPREEQYNST YRVVSVLTVLHQDWLNGKEY KCKVSNKALPAPIEKTISKA KGQPREPQVYTLPPSRDELT KNQVSLTCLVKGFYPSDIAV EWESNGQPENNYKTTPPVLD SDGSFFLYSKLTVDKSRWQQ GNVFSCSVMHEALHNHYTQK SLSLSPGENLYFQGPGGGSH HHHHH

Data sets:
Data typeCount
13C chemical shifts110
1H chemical shifts330

Time Domain Data

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Fc monomer, chain 11
2Fc monomer, chain 21

Entities:

Entity 1, Fc monomer, chain 1 245 residues - Formula weight is not available

1   METASPLYSTHRHISTHRCYSPROPROCYS
2   PROALAPROGLULEULEUGLYGLYPROSER
3   VALPHELEUPHEPROPROLYSPROLYSASP
4   THRLEUMETILESERARGTHRPROGLUVAL
5   THRCYSVALVALVALASPVALSERHISGLU
6   ASPPROGLUVALLYSPHEASNTRPTYRVAL
7   ASPGLYVALGLUVALHISASNALALYSTHR
8   LYSPROARGGLUGLUGLNTYRASNSERTHR
9   TYRARGVALVALSERVALLEUTHRVALLEU
10   HISGLNASPTRPLEUASNGLYLYSGLUTYR
11   LYSCYSLYSVALSERASNLYSALALEUPRO
12   ALAPROILEGLULYSTHRILESERLYSALA
13   LYSGLYGLNPROARGGLUPROGLNVALTYR
14   THRLEUPROPROSERARGASPGLULEUTHR
15   LYSASNGLNVALSERLEUTHRCYSLEUVAL
16   LYSGLYPHETYRPROSERASPILEALAVAL
17   GLUTRPGLUSERASNGLYGLNPROGLUASN
18   ASNTYRLYSTHRTHRPROPROVALLEUASP
19   SERASPGLYSERPHEPHELEUTYRSERLYS
20   LEUTHRVALASPLYSSERARGTRPGLNGLN
21   GLYASNVALPHESERCYSSERVALMETHIS
22   GLUALALEUHISASNHISTYRTHRGLNLYS
23   SERLEUSERLEUSERPROGLYGLUASNLEU
24   TYRPHEGLNGLYPROGLYGLYGLYSERHIS
25   HISHISHISHISHIS

Samples:

sample_1: Non-glycosylated IgG1 Fc fragment, [U-13C; U-15N], 0.3 mM; NaOAc 10 mM

sample_2: Non-glycosylated IgG1 Fc fragment, [U-13C; U-15N], 0.7 mM; NaOAc 10 mM

sample_3: Non-glycosylated IgG1 Fc fragment, Ala, Ile-d1, Met, Thr, Val-g1/g2: 13CH3, 1.6 mM; NaOAc 10 mM

sample_4: Non-glycosylated IgG1 Fc fragment, Leu-d1,d2: 13CH3, 0.79 mM; NaOAc 10 mM

sample_5: Non-glycosylated IgG1 Fc fragment, Val-g1,g2: 13CH3, 0.23 mM; NaOAc 10 mM

sample_6: Non-glycosylated IgG1 Fc fragment, Met, Val-g1/g2: 13CH3, 0.16 mM; NaOAc 10 mM

sample_7: Non-glycosylated IgG1 Fc fragment, Ile-d1, Thr: 13CH3, 0.16 mM; NaOAc 10 mM

sample_8: Non-glycosylated IgG1 Fc fragment, Ala: 13CH3, 0.23 mM; NaOAc 10 mM

sample_conditions_1: ionic strength: 0.01 M; pH: 5; pressure: 1 atm; temperature: 323 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
2D 1H-13C CT-SOFASTsample_2isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_2isotropicsample_conditions_1
3D CCH methyl NOESYsample_3isotropicsample_conditions_1
3D CCH methyl NOESYsample_4isotropicsample_conditions_1
2D 1H-13C CT-SOFASTsample_4isotropicsample_conditions_1
2D 1H-13C SOFASTsample_4isotropicsample_conditions_1
3D CCH methyl NOESYsample_5isotropicsample_conditions_1
2D 1H-13C SOFASTsample_6isotropicsample_conditions_1
2D 1H-13C SOFASTsample_7isotropicsample_conditions_1
2D 1H-13C SOFASTsample_8isotropicsample_conditions_1

Software:

TOPSPIN - collection, processing

CcpNMR - chemical shift assignment, data analysis

Chimera - data analysis

NMRPipe - processing

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE NEO 700 MHz
  • Bruker AVANCE NEO 850 MHz
  • Bruker AVANCE NEO 950 MHz