BMRB Entry 52243

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52243

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Title:
Enabling Site-Specific NMR Investigations of Therapeutic Fab using a Cell-Free Based Isotopic Labeling Approach: Application to anti-LAMP1 Fab.
Deposition date:
2023-12-14
Original release date:
2024-08-28
Authors:
Giraud, Arthur; Imbert, Lionel; Favier, Adrien; Henot, Faustine; Duffieux, Francis; Samson, Camille; Frances, Oriane; Crublet, Elodie; Boisbouvier, Jerome
Citation:

Citation: Giraud, Arthur; Imbert, Lionel; Favier, Adrien; Henot, Faustine; Duffieux, Francis; Samson, Camille; Samson, Oriane; Crublet, Elodie; Boisbouvier, Jerome. "Enabling site-specific NMR investigations of therapeutic Fab using a cell-free based isotopic labeling approach: application to anti-LAMP1 Fab"  J. Biomol. NMR 78, 73-86 (2024).
PubMed: 38546905

Assembly members:

Assembly members:
entity_1, polymer, 214 residues, Formula weight is not available
entity_2, polymer, 227 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 2.4d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GDIQMTQSPSSLSASVGDRV TITCKASQDIDRYMAWYQDK PGKAPRLLIHDTSTLQSGVP SRFSGSGSGRDYTLTISNLE PEDFATYYCLQYDNLWTFGG GTKVEIKRTVAAPSVFIFPP SDEQLKSGTASVVCLLNNFY PREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLT LSKADYEKHKVYACEVTHQG LSSPVTKSFNRGEC
entity_2: GQVQLVQSGAEVKKPGSSVK VSCKASGYIFTNYNIHWVKK SPGQGLEWIGAIYPGNGDAP YSQKFQGKATLTADTSTSTT YMELSSLRSEDTAVYYCVRA NWDVAFAYWGQGTLVTVSSA STKGPSVFPLAPSSKSTSGG TAALGCLVKDYFPEPVTVSW NSGALTSGVHTFPAVLQSSG LYSLSSVVTVPSSSLGTQTY ICNVNHKPSNTKVDKKVEPK SCDKTHT

Data sets:
Data typeCount
13C chemical shifts1176
15N chemical shifts372
1H chemical shifts372

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Anti-LAMP1 Fab fragment light chain1
2Anti-LAMP1 Fab fragment heavy chain2

Entities:

Entity 1, Anti-LAMP1 Fab fragment light chain 214 residues - Formula weight is not available

The sequence of the Fab fragment is composed with two amino acids chains: the light chain and the heavy chain. The two chain are linked thanks to a disulfide bond between two cysteines at their C-terminal.

1   GLYASPILEGLNMETTHRGLNSERPROSER
2   SERLEUSERALASERVALGLYASPARGVAL
3   THRILETHRCYSLYSALASERGLNASPILE
4   ASPARGTYRMETALATRPTYRGLNASPLYS
5   PROGLYLYSALAPROARGLEULEUILEHIS
6   ASPTHRSERTHRLEUGLNSERGLYVALPRO
7   SERARGPHESERGLYSERGLYSERGLYARG
8   ASPTYRTHRLEUTHRILESERASNLEUGLU
9   PROGLUASPPHEALATHRTYRTYRCYSLEU
10   GLNTYRASPASNLEUTRPTHRPHEGLYGLY
11   GLYTHRLYSVALGLUILELYSARGTHRVAL
12   ALAALAPROSERVALPHEILEPHEPROPRO
13   SERASPGLUGLNLEULYSSERGLYTHRALA
14   SERVALVALCYSLEULEUASNASNPHETYR
15   PROARGGLUALALYSVALGLNTRPLYSVAL
16   ASPASNALALEUGLNSERGLYASNSERGLN
17   GLUSERVALTHRGLUGLNASPSERLYSASP
18   SERTHRTYRSERLEUSERSERTHRLEUTHR
19   LEUSERLYSALAASPTYRGLULYSHISLYS
20   VALTYRALACYSGLUVALTHRHISGLNGLY
21   LEUSERSERPROVALTHRLYSSERPHEASN
22   ARGGLYGLUCYS

Entity 2, Anti-LAMP1 Fab fragment heavy chain 227 residues - Formula weight is not available

The sequence of the Fab fragment is composed with two amino acids chains: the light chain and the heavy chain. The two chain are linked thanks to a disulfide bond between two cysteines at their C-terminal.

1   GLYGLNVALGLNLEUVALGLNSERGLYALA
2   GLUVALLYSLYSPROGLYSERSERVALLYS
3   VALSERCYSLYSALASERGLYTYRILEPHE
4   THRASNTYRASNILEHISTRPVALLYSLYS
5   SERPROGLYGLNGLYLEUGLUTRPILEGLY
6   ALAILETYRPROGLYASNGLYASPALAPRO
7   TYRSERGLNLYSPHEGLNGLYLYSALATHR
8   LEUTHRALAASPTHRSERTHRSERTHRTHR
9   TYRMETGLULEUSERSERLEUARGSERGLU
10   ASPTHRALAVALTYRTYRCYSVALARGALA
11   ASNTRPASPVALALAPHEALATYRTRPGLY
12   GLNGLYTHRLEUVALTHRVALSERSERALA
13   SERTHRLYSGLYPROSERVALPHEPROLEU
14   ALAPROSERSERLYSSERTHRSERGLYGLY
15   THRALAALALEUGLYCYSLEUVALLYSASP
16   TYRPHEPROGLUPROVALTHRVALSERTRP
17   ASNSERGLYALALEUTHRSERGLYVALHIS
18   THRPHEPROALAVALLEUGLNSERSERGLY
19   LEUTYRSERLEUSERSERVALVALTHRVAL
20   PROSERSERSERLEUGLYTHRGLNTHRTYR
21   ILECYSASNVALASNHISLYSPROSERASN
22   THRLYSVALASPLYSLYSVALGLUPROLYS
23   SERCYSASPLYSTHRHISTHR

Samples:

sample_1: Anti-LAMP1 Fab fragment light chain, [U-100% 13C; U-100% 15N; U-80% 2H], 300 uM; Anti-LAMP1 Fab fragment heavy chain, [U-100% 13C; U-100% 15N; U-80% 2H], 300 uM; MES 50 mM; sodium chloride 100 mM; AEBSF protease inhibitor 1 tablet/100mL

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D BT_HNCOsample_1isotropicsample_conditions_1
3D BT_HNCAsample_1isotropicsample_conditions_1
3D BT_HN(CA)COsample_1isotropicsample_conditions_1
3D BT_HNCACBsample_1isotropicsample_conditions_1
3D BT_HN(CO)CAsample_1isotropicsample_conditions_1
3D BT_HN(COCA)CBsample_1isotropicsample_conditions_1

Software:

CcpNMR v3.0 - chemical shift assignment

TOPSPIN - collection

NMRPipe - processing

NMR spectrometers:

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

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks