BMRBj - BMREntryMaster

Found 1 Document (0.787 seconds)

BMRB: 34408

6RVA

STRUCTURE OF [ASP58]-IGF-I ANALOGUE

Authors

Jiracek, J., Zakova, L., Socha, O.

Assembly

Insulin-like growth factor I

Entity

1. Insulin-like growth factor I (polymer, Thiol state: all disulfide bound), 71 monomers, 7697.703 Da Detail

GGPETLCGAE LVDALQFVCG DRGFYFNKPT GYGSSSRRAP QTGIVDECCF RSCDLRRLDM YCAPLKPAKS A

Formula weight

7697.703 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS49:SG
2	disulfide	sing	1:CYS19:SG	1:CYS62:SG
3	disulfide	sing	1:CYS48:SG	1:CYS53:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.9 %, Completeness (bb): 79.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.9 % (672 of 782)	98.0 % (400 of 408)	66.9 % (204 of 305)	98.6 % (68 of 69)
Backbone	79.1 % (329 of 416)	96.6 % (140 of 145)	60.5 % (124 of 205)	98.5 % (65 of 66)
Sidechain	93.5 % (401 of 429)	98.9 % (260 of 263)	84.7 % (138 of 163)	100.0 % (3 of 3)
Aromatic	68.8 % (44 of 64)	93.8 % (30 of 32)	43.8 % (14 of 32)
Methyl	98.3 % (57 of 58)	96.6 % (28 of 29)	100.0 % (29 of 29)

1. entity 1

GGPETLCGAE LVDALQFVCG DRGFYFNKPT GYGSSSRRAP QTGIVDECCF RSCDLRRLDM YCAPLKPAKS A

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313.15 K, pH 3.0, Details 0.18 mM [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	[L-Asp58]-IGF-1 analogue	natural abundance	0.18 mM
2	sodium azide	natural abundance	0.01 %
3	acetic acid	[U-2H]	50 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313.15 K, pH 3.0, Details 0.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	[L-Asp58]-IGF-1 analogue	[U-13C; U-15N]	0.05 mM
5	sodium azide	natural abundance	0.01 %
6	acetic acid	[U-2H]	50 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 313.15 K, pH 3.0, Details 0.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 100% D2O

#	Name	Isotope labeling	Concentration
7	[L-Asp58]-IGF-1 analogue	[U-13C; U-15N]	0.05 mM
8	sodium azide	natural abundance	0.01 %
9	acetic acid	[U-2H]	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	acetate	methyl protons	2.05 ppm	internal	indirect	0.2514495
¹H	acetate	methyl protons	2.05 ppm	internal	direct	1.0
¹⁵N	acetate	methyl protons	2.05 ppm	internal	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	acetate	methyl protons	2.05 ppm	internal	indirect	0.2514495
¹H	acetate	methyl protons	2.05 ppm	internal	direct	1.0
¹⁵N	acetate	methyl protons	2.05 ppm	internal	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	acetate	methyl protons	2.05 ppm	internal	indirect	0.2514495
¹H	acetate	methyl protons	2.05 ppm	internal	direct	1.0
¹⁵N	acetate	methyl protons	2.05 ppm	internal	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6RVA, Strand ID: X Detail

Release date

2019-10-10

Citation

Mutations at hypothetical binding site 2 in insulin and insulin-like growth factors 1 and 2 result in receptor- and hormone-specific responses
Machackova, K., Mlcochova, K., Potalitsyn, P., Hankova, K., Socha, O., Budesinsky, M., Muzdalo, A., Lepsik, M., Cernekova, M., Radosavljevic, J., Fabry, M., Mitrova, K., Chrudinova, M., Lin, J., Yurenko, Y., Hobza, P., Selicharova, I., Akova, L., Jiracek, J.
J. Biol. Chem. (2019), 294, 17371-17382, PubMed 31558604 , DOI 10.1074/jbc.RA119.010072 , Abstract

Related entities 1. Insulin-like growth factor I, : 1 : 194 entities Detail

Interaction partners 1. Insulin-like growth factor I, : 9 interactors Detail

More details for 9 interactors identified by 4 citations

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34408_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:7:CYS:SG	1:49:CYS:SG	oxidized, CB 45.084 ppm	unknown	n/a
1:19:CYS:SG	1:62:CYS:SG	oxidized, CA 54.157, CB 37.622 ppm	unknown, CA 53.259 ppm	n/a
1:48:CYS:SG	1:53:CYS:SG	unknown, CA 56.763 ppm	unknown, CA 54.062 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34408_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	724		100.0 (chain: 1, length: 71)
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: 71, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 461
  - ¹³C chemical shifts: 189
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	408	403	98.8
¹³C chemical shifts	305	189	62.0
¹⁵N chemical shifts	75	74	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	145	143	98.6
¹³C chemical shifts	142	53	37.3
¹⁵N chemical shifts	66	65	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	263	260	98.9
¹³C chemical shifts	163	136	83.4
¹⁵N chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	29	96.7
¹³C chemical shifts	30	30	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	30	93.8
¹³C chemical shifts	32	14	43.8

Keywords HORMONE, IGF-I ANALOGUE

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Found 1 Document (0.787 seconds)

BMRB: 34408

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Insulin-like growth factor I, : 1 : 194 entities Detail

Interaction partners 1. Insulin-like growth factor I, : 9 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail