BMRBj - BMREntryMaster

Found 1 Document (0.568 seconds)

BMRB: 34515

6YW8

NMR solution structure of unbound recombinant human Nerve Growth Factor (rhNGF)

Authors

Golic Grdadolnik, S., Paoletti, F.

Assembly

Beta-nerve growth factor

Entity

1. Beta-nerve growth factor (polymer, Thiol state: all disulfide bound), 118 monomers, 13266.97 × 2 Da Detail

SSSHPIFHRG EFSVCDSVSV WVGDKTTATD IKGKEVMVLG EVNINNSVFK QYFFETKCRD PNPVDSGCRG IDSKHWNSYC TTTHTFVKAL TMDGKQAAWR FIRIDTACVC VLSRKAVR

Total weight

26533.94 Da

Max. entity weight

13266.97 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS15:SG	1:CYS80:SG
2	disulfide	sing	1:CYS58:SG	1:CYS108:SG
3	disulfide	sing	1:CYS68:SG	1:CYS110:SG
4	disulfide	sing	1:CYS15:SG	1:CYS80:SG
5	disulfide	sing	1:CYS58:SG	1:CYS108:SG
6	disulfide	sing	1:CYS68:SG	1:CYS110:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 82.1 %, Completeness (bb): 83.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.1 % (1119 of 1363)	91.8 % (641 of 698)	67.7 % (361 of 533)	88.6 % (117 of 132)
Backbone	83.2 % (584 of 702)	96.7 % (232 of 240)	70.3 % (244 of 347)	93.9 % (108 of 115)
Sidechain	82.9 % (640 of 772)	89.3 % (409 of 458)	74.7 % (222 of 297)	52.9 % (9 of 17)
Aromatic	27.5 % (38 of 138)	50.7 % (35 of 69)	0.0 % (0 of 66)	100.0 % (3 of 3)
Methyl	99.2 % (119 of 120)	100.0 % (60 of 60)	98.3 % (59 of 60)

1. entity 1

SSSHPIFHRG EFSVCDSVSV WVGDKTTATD IKGKEVMVLG EVNINNSVFK QYFFETKCRD PNPVDSGCRG IDSKHWNSYC TTTHTFVKAL TMDGKQAAWR FIRIDTACVC VLSRKAVR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 0.1 mM [U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Nerve Growth Factor	[U-99% 15N]		0.1 mM
2	HEPES	natural abundance		50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Nerve Growth Factor	[U-99% 13C; U-99% 15N]		0.1 mM
4	HEPES	natural abundance		50 mM

Release date

2020-05-10

Citation

Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions
Paoletti, F., Merzel, F., Cassetta, A., Ogris, I., Covaceuszach, S., Grdadolnik, J., Lamba, D., Golic Grdadolnik, S.
Comput. Struct. Biotechnol. J. (2021), 19, 2938-2949, PubMed 34136093 , DOI 10.1016/j.csbj.2021.05.009 , Abstract

Related entities 1. Beta-nerve growth factor, : 1 : 11 : 2 : 131 entities Detail

Interaction partners 1. Beta-nerve growth factor, : 7 interactors Detail

More details for 7 interactors identified by 3 citations

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34515_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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:15:CYS:SG	1:80:CYS:SG	oxidized, CA 54.432, CB 47.1 ppm	oxidized, CA 54.612, CB 42.875 ppm	n/a
1:58:CYS:SG	1:108:CYS:SG	oxidized, CA 54.172, CB 40.896 ppm	oxidized, CA 54.873, CB 40.949 ppm	n/a
1:68:CYS:SG	1:110:CYS:SG	oxidized, CA 54.258, CB 42.811 ppm	oxidized, CA 54.444, CB 42.212 ppm	n/a
2:15:CYS:SG	2:80:CYS:SG	oxidized, CA 54.432, CB 47.1 ppm	oxidized, CA 54.612, CB 42.875 ppm	n/a
2:58:CYS:SG	2:108:CYS:SG	oxidized, CA 54.172, CB 40.896 ppm	oxidized, CA 54.873, CB 40.949 ppm	n/a
2:68:CYS:SG	2:110:CYS:SG	oxidized, CA 54.258, CB 42.811 ppm	oxidized, CA 54.444, CB 42.212 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34515_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2416		98.3 (chain: 1, length: 118)
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: 118, Sequence coverage: 98.3%
- Total number of assignments
  - ¹H chemical shifts: 1530
  - ¹³C chemical shifts: 658
  - ¹⁵N chemical shifts: 228
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
85	THR	HG1	6.419

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	698	640	91.7
¹³C chemical shifts	533	329	61.7
¹⁵N chemical shifts	132	114	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	240	231	96.3
¹³C chemical shifts	236	108	45.8
¹⁵N chemical shifts	115	105	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	458	409	89.3
¹³C chemical shifts	297	221	74.4
¹⁵N chemical shifts	17	9	52.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	62	100.0
¹³C chemical shifts	62	61	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	35	50.7
¹³C chemical shifts	66	0	0.0
¹⁵N chemical shifts	3	3	100.0

Keywords CELL CYCLE, cystin-knot, homodimer, human NGF, unbound structure

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Found 1 Document (0.568 seconds)

BMRB: 34515

Sample #1

Sample #2

Related entities 1. Beta-nerve growth factor, : 1 : 11 : 2 : 131 entities Detail

Interaction partners 1. Beta-nerve growth factor, : 7 interactors Detail

Experiments performed 5 experiments Detail

Instrument

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Chemical shift validation 3 contents Detail