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BMRB: 34381

6R2X

NMR structure of Chromogranin A (F39-D63)

Authors

Nardelli, F., Quilici, G., Ghitti, M., Curnis, F., Gori, A., Berardi, A., Corti, A., Musco, G.

Assembly

Chromogranin-A

Entity

1. Chromogranin-A (polymer, Thiol state: not present), 25 monomers, 3037.429 Da Detail

FETLRGDERI LSILRHQNLL KELQD

Formula weight

3037.429 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 99.4 %, Completeness (bb): 98.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	99.4 % (313 of 315)	99.4 % (166 of 167)	100.0 % (120 of 120)	96.4 % (27 of 28)
Backbone	98.7 % (148 of 150)	98.0 % (50 of 51)	100.0 % (74 of 74)	96.0 % (24 of 25)
Sidechain	100.0 % (189 of 189)	100.0 % (116 of 116)	100.0 % (70 of 70)	100.0 % (3 of 3)
Aromatic	100.0 % (14 of 14)	100.0 % (7 of 7)	100.0 % (7 of 7)
Methyl	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)

1. entity 1

FETLRGDERI LSILRHQNLL KELQD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	Chromogranin A	natural abundance		0.5 mM
5	sodium chloride	natural abundance		100 mM
6	sodium phosphate	natural abundance		20 mM

Sample #3

Solvent system 100% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Chromogranin A	[U-13C; U-15N]		0.5 mM
8	sodium chloride	natural abundance		100 mM
9	sodium phosphate	natural abundance		20 mM

Sample #4

Solvent system 100% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
10	Chromogranin A	natural abundance		0.5 mM
11	sodium chloride	natural abundance		100 mM
12	sodium phosphate	natural abundance		20 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 6R2X, Strand ID: A Detail

Release date

2019-03-21

Citation

A stapled chromogranin A-derived peptide is a potent dual ligand for integrins αvβ6 and αvβ8
Nardelli, F., Ghitti, M., Quilici, G., Gori, A., Luo, Q., Berardi, A., Sacchi, A., Monieri, M., Bergamaschi, G., Bermel, W., Chen, F., Corti, A., Curnis, F., Musco, G.
Chem. Commun. (Camb). (2019), 55, 14777-14780, PubMed 31755501 , DOI 10.1039/c9cc08518a , Abstract

Related entities 1. Chromogranin-A, : 1 : 5 : 7 entities Detail

Interaction partners 1. Chromogranin-A, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	Chromogranin A	natural abundance		0.5 mM
5	sodium chloride	natural abundance		100 mM
6	sodium phosphate	natural abundance		20 mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	Chromogranin A	natural abundance		0.5 mM
5	sodium chloride	natural abundance		100 mM
6	sodium phosphate	natural abundance		20 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
10	Chromogranin A	natural abundance		0.5 mM
11	sodium chloride	natural abundance		100 mM
12	sodium phosphate	natural abundance		20 mM

4 2D 1H-13C HSQC

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

6 3D HNCA

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

7 3D HNCO

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

8 3D HNHA

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

9 3D 1H-13C NOESY

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Chromogranin A	[U-13C; U-15N]		0.5 mM
8	sodium chloride	natural abundance		100 mM
9	sodium phosphate	natural abundance		20 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance-600 - 600 MHz triple-resonance TCI cryo-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 280 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Chromogranin A, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Chromogranin A	[U-13C; U-15N]		0.5 mM
2	sodium chloride	natural abundance		100 mM
3	sodium phosphate	natural abundance		20 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34381_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	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr34381_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	363		100.0 (chain: 1, length: 25)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 25, Sequence coverage: 100.0%

--------10--------20-----
FETLRGDERILSILRHQNLLKELQD
|||||||||||||||||||||||||
FETLRGDERILSILRHQNLLKELQD

Total number of assignments
- ¹H chemical shifts: 200
- ¹³C chemical shifts: 133
- ¹⁵N chemical shifts: 30

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	PHE	CG	136.367
2	GLU	CD	184.15
5	ARG	CZ	159.567
7	ASP	CG	180.078
8	GLU	CD	183.986
9	ARG	CZ	159.558
15	ARG	CZ	159.511
16	HIS	CG	132.76
17	GLN	CD	180.214
18	ASN	CG	176.757
22	GLU	CD	184.005
24	GLN	CD	180.612
25	ASP	CG	180.08

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	167	166	99.4
¹³C chemical shifts	120	120	100.0
¹⁵N chemical shifts	31	30	96.8

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	50	98.0
¹³C chemical shifts	50	50	100.0
¹⁵N chemical shifts	25	24	96.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	116	116	100.0
¹³C chemical shifts	70	70	100.0
¹⁵N chemical shifts	6	6	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	17	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	7	100.0

Tautomeric state of HIS
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 HORMONE, fragment of Chromogranin A, interactors, ligand of alpha V beta 6