BMRB Entry 53420

Name: Chemical Shift Assignment of ipilimumab variable light domain (VL)
Published: 2025-11-14

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53420

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Chemical Shift Assignment of ipilimumab variable light domain (VL)

Deposition date:

2025-11-06

Original release date:

2025-11-14

Authors:

Henot, Faustine; Vibert, Beatrice; Boisbouvier, Jerome; Frances, Oriane

Citation:

Citation: Henot, Faustine; Vibert, Beatrice; Giraud, Arthur; Dbira, Sarra; Imbert, Lionel; Favier, Adrien; Guntert, Peter; Clavier, Severine; Crublet, Elodie; Doyen, Camille; Boisbouvier, Jerome; Frances, Oriane. "A fast and efficient strategy for the NMR assignment of Fab methyl groups" J. Biomol. NMR ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 136 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: MSGSHHHHHHSSGIEGRGRE NLYFQGEIVLTQSPGTLSLS PGERATLSCRASQSVGSSYL AWYQQKPGQAPRLLIYGAFS RATGIPDRFSGSGSGTDFTL TISRLEPEDFAVYYCQQYGS SPWTFGQGTKVEIKRT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	288
15N chemical shifts	77
1H chemical shifts	248

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VL-ipilimumab	1

Entities:

Entity 1, VL-ipilimumab 136 residues - Formula weight is not available

1

MET

SER

GLY

SER

HIS

2

SER

GLY

ILE

GLU

GLY

ARG

GLY

ARG

GLU

3

ASN

LEU

TYR

PHE

GLN

GLY

GLU

ILE

VAL

LEU

4

THR

GLN

SER

PRO

GLY

THR

LEU

SER

LEU

SER

5

PRO

GLY

GLU

ARG

ALA

THR

LEU

SER

CYS

ARG

6

ALA

SER

GLN

SER

VAL

GLY

SER

TYR

LEU

7

ALA

TRP

TYR

GLN

LYS

PRO

GLY

GLN

ALA

8

PRO

ARG

LEU

ILE

TYR

GLY

ALA

PHE

SER

9

ARG

ALA

THR

GLY

ILE

PRO

ASP

ARG

PHE

SER

10

GLY

SER

GLY

SER

GLY

THR

ASP

PHE

THR

LEU

11

THR

ILE

SER

ARG

LEU

GLU

PRO

GLU

ASP

PHE

12

ALA

VAL

TYR

CYS

GLN

TYR

GLY

SER

13

SER

PRO

TRP

THR

PHE

GLY

GLN

GLY

THR

LYS

14

VAL

GLU

ILE

LYS

ARG

THR

Samples:

sample_1: Variable Light Domain (VL) from ipilimumab, [Met, Ala: 13CH3], 140 uM; MES 50 mM; NaCl 100 mM

sample_2: Variable Light Domain (VL) from ipilimumab, [Met / Ile-d1 / V-pro-S 13CH3], 95 uM; MES 50 mM; NaCl 100 mM

sample_3: Variable Light Domain (VL) from ipilimumab, [Met / Thr 13CH3], 108 uM; MES 50 mM; NaCl 100 mM

sample_4: Variable Light Domain (VL) from ipilimumab, [Met / Val-proS/Val-proR 13CH3], 45 uM; MES 50 mM; NaCl 100 mM

sample_5: Variable Light Domain (VL) from ipilimumab, [Met / Leu-proS 13CH3], 16 uM; MES 50 mM; NaCl 100 mM

sample_6: Variable Light Domain (VL) from ipilimumab, [U-100% 13C; U-100% 15N], 370 uM; MES 50 mM; NaCl 100 mM

sample_7: Variable Light Domain (VL) from ipilimumab, [U-100% 13C; U-100% 15N], 1.38 mM; MES 50 mM; NaCl 100 mM

sample_conditions_1: ionic strength: 0.125 M; pH: 6.9; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 0.125 M; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_6	isotropic	sample_conditions_2
2D 1H-15N TROSY	sample_6	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_2
3D HN(COCA)CB	sample_6	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_2
3D HN(CA)CO	sample_6	isotropic	sample_conditions_2
3D HNCA	sample_6	isotropic	sample_conditions_2
3D HN(CO)CA	sample_6	isotropic	sample_conditions_2
HN(CA)CB	sample_6	isotropic	sample_conditions_2
3D HNCO	sample_6	isotropic	sample_conditions_2
NOESY HCH	sample_7	isotropic	sample_conditions_2

Software:

CcpNMR - data analysis, peak picking

NMRPipe - processing

TOPSPIN - collection, processing

Chimera - data analysis

NMR spectrometers:

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

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