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BMRB: 36293

6L8R

membrane-bound PD-L1-CD

Authors

Maorong, W., Bin, W., Bo, O.

Assembly

Programmed cell death 1 ligand 1

Entity

1. Programmed cell death 1 ligand 1 (polymer, Thiol state: all free), 33 monomers, 3788.296 Da Detail

GPRLRKGRMM DVKKCGIQDT NSKKQSDTHL EET

Formula weight

3788.296 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.0 %, Completeness: 95.1 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.1 % (371 of 390)	94.7 % (198 of 209)	94.4 % (135 of 143)	100.0 % (38 of 38)
Backbone	96.4 % (189 of 196)	95.6 % (65 of 68)	95.8 % (92 of 96)	100.0 % (32 of 32)
Sidechain	94.2 % (211 of 224)	94.3 % (133 of 141)	93.5 % (72 of 77)	100.0 % (6 of 6)
Aromatic	0.0 % (0 of 4)	0.0 % (0 of 2)	0.0 % (0 of 2)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. Programmed cell death 1 ligand 1

GPRLRKGRMM DVKKCGIQDT NSKKQSDTHL EET

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C PD-L1-CD, 60 mM 2H DMPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	PD-L1-CD	[U-13C; U-15N]	protein	0.5 mM
7	DHPC	[U-2H]		85 mM
8	DMPG	[U-2H]		60 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_2H PD-L1-CD, 60 mM POPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
11	PD-L1-CD	[U-15N; U-2H]	protein	0.5 mM
12	DHPC	[U-2H]		85 mM
13	POPG	natural abundance		60 mM
14	H2O	natural abundance	solvent	90 %
15	D2O	[U-2H]	solvent	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 6L8R, Strand ID: A Detail

Release date

2020-09-22

Citation

PD-L1 degradation is regulated by electrostatic membrane association of its cytoplasmic domain
Wen, M., Cao, Y., Wu, B., Xiao, T., Cao, R., Wang, Q., Liu, X., Xue, H., Yu, Y., Lin, J., Xu, C., Xu, J., OuYang, B.
Nat. Commun. (2021), 12, 5106-5106, PubMed 34429434 , DOI 10.1038/s41467-021-25416-7 , Abstract

Related entities 1. Programmed cell death 1 ligand 1, : 1 : 2 : 3 entities Detail

Interaction partners 1. Programmed cell death 1 ligand 1, : 6 interactors Detail

More details for 6 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 3D HNCO

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 3D HNCA

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 3D HN(CO)CA

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 3D HNCACB

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

6 3D HNCACO

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PD-L1-CD	[U-13C; U-15N; U-2H]	protein	0.5 mM
2	DHPC	natural abundance		85 mM
3	DMPG	natural abundance		60 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

7 3D 1H-13C NOESY

Instrument

Varian DD2 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C PD-L1-CD, 60 mM 2H DMPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	PD-L1-CD	[U-13C; U-15N]	protein	0.5 mM
7	DHPC	[U-2H]		85 mM
8	DMPG	[U-2H]		60 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

8 3D 1H-15N NOESY

Instrument

Varian DD2 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C PD-L1-CD, 60 mM 2H DMPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	PD-L1-CD	[U-13C; U-15N]	protein	0.5 mM
7	DHPC	[U-2H]		85 mM
8	DMPG	[U-2H]		60 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

9 2D 1H-13C HSQC

Instrument

Varian DD2 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C PD-L1-CD, 60 mM 2H DMPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	PD-L1-CD	[U-13C; U-15N]	protein	0.5 mM
7	DHPC	[U-2H]		85 mM
8	DMPG	[U-2H]		60 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

10 3D 1H-15N NOESY for lipid NOE

Instrument

Varian DD2 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_2H PD-L1-CD, 60 mM POPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
11	PD-L1-CD	[U-15N; U-2H]	protein	0.5 mM
12	DHPC	[U-2H]		85 mM
13	POPG	natural abundance		60 mM
14	H2O	natural abundance	solvent	90 %
15	D2O	[U-2H]	solvent	10 %

11 3D HCCH-TOCSY

Instrument

Varian DD2 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 0.5 mM 15N_13C PD-L1-CD, 60 mM 2H DMPG, 85 mM 2H DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
6	PD-L1-CD	[U-13C; U-15N]	protein	0.5 mM
7	DHPC	[U-2H]		85 mM
8	DMPG	[U-2H]		60 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr36293_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr36293_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	394		93.9 (chain: 1, length: 33)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 33, Sequence coverage: 93.9%
- Total number of assignments
  - ¹H chemical shifts: 223
  - ¹³C chemical shifts: 134
  - ¹⁵N chemical shifts: 37
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords IMMUNOSUPPRESSANT, PD-L1, cytoplasmic domain, membrane-bound, stability