BMRBj - BMREntryMaster

Found 1 Document (1.739 seconds)

BMRB: 6875

3OJM

Solution structure of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue

Authors

Canales, A., Lozano, R., Nieto, P.M., Martin-Lomas, M., Gimenez-Gallego, G., Jimenez-Barbero, J.

Assembly

acidic fibroblast growht factor

Entity

1. FGF-1 (polymer, Thiol state: all free), 139 monomers, 15688.49 Da Detail

NLPPGNYKKP KLLYCSNGGH FLRILPDGTV DGTRDRSDQH IQLQLSAESV GEVYIKSTET GQYLAMDTDG LLYGSQTPNE ECLFLERLEE NHYNTYISKK HAEKNWFVGL KKNGSCKRGP RTHYGQKAIL FLPLPVSSD

2. HLHS (polymer), 7 monomers, 1514.287 Da

Total weight

17202.777 Da

Max. entity weight

15688.49 Da

Entity Connection

covalent 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	2:IDS1:O4	2:GNS2:C1
2	covalent	sing	2:GNS2:O4	2:IDR3:C1
3	covalent	sing	2:IDR3:O4	2:NGY4:C1
4	covalent	sing	2:NGY4:O4	2:IDS5:C1
5	covalent	sing	2:IDS5:O4	2:GNS6:C1
6	covalent	sing	2:GNS6:O4	2:IPA7:C2

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

Simulated annealing, restrained molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.1 %, Completeness: 66.6 %, Completeness (bb): 78.5 % Detail

Polymer type: polypeptide(L) polysaccharide(D)

	Total	¹H	¹³C	¹⁵N
All	66.6 % (1091 of 1638)	79.2 % (680 of 859)	45.0 % (285 of 633)	86.3 % (126 of 146)
Backbone	78.5 % (642 of 818)	93.6 % (265 of 283)	63.6 % (257 of 404)	91.6 % (120 of 131)
Sidechain	49.7 % (470 of 946)	72.0 % (415 of 576)	13.8 % (49 of 355)	40.0 % (6 of 15)
Aromatic	44.1 % (60 of 136)	88.2 % (60 of 68)	0.0 % (0 of 67)	0.0 % (0 of 1)
Methyl	54.5 % (72 of 132)	89.4 % (59 of 66)	19.7 % (13 of 66)

1. FGF-1

NLPPGNYKKP KLLYCSNGGH FLRILPDGTV DGTRDRSDQH IQLQLSAESV GEVYIKSTET GQYLAMDTDG LLYGSQTPNE ECLFLERLEE NHYNTYISKK HAEKNWFVGL KKNGSCKRGP RTHYGQKAIL FLPLPVSSD

Show sample condition

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2ERM, Strand ID: A Detail

Release date

2006-11-15

Citation 1

Solution NMR structure of a human FGF-1 monomer, activated by a hexasaccharide heparin-analogue
Canales, A., Lozano, R., Lopez-Mendez, B., Angulo, J., Ojeda, R., Nieto, P.M., Martin-Lomas, M., Gimenez-Gallego, G., Jimenez-Barbero, J.
FEBS J. (2006), 273, 4716-4727, PubMed 16995857 , DOI 10.1111/j.1742-4658.2006.05474.x , Abstract

Show more 2 citaions

Citation 2

1H NMR structural characterization of a nonmitogenic, vasodilatory, ischemia-protector and neuromodulatory acidic fibroblast growth factor
Lozano, R.M., Pineda-Lucena, A., Gonzalez, C., Angeles Jimenez, M., Cuevas, P., Redondo-Horcajo, M., Sanz, J.M., Rico, M., Gimenez-Gallego, G.
Biochemistry (2000), 39, 4982-4993, PubMed 10819962 , DOI: , Abstract

Citation 3

Conformational flexibility of a synthetic glycosylaminoglycan bound to a fibroblast growth factor. FGF-1 recognizes both the (1)C(4) and (2)S(O) conformations of a bioactive heparin-like hexasaccharide
Canales, A., Angulo, J., Ojeda, R., Bruix, M., Fayos, R., Lozano, R., Gimenez-Gallego, G., Martin-Lomas, M., Nieto, P.M., Jiminez-Barbero, J.
J. Am. Chem. Soc. (2005), 127, 5778-5779, PubMed 15839662 , DOI 10.1021/ja043363y , Abstract

Hide non-primary 2 citaions

Related entities 1. FGF-1, : 1 : 15 : 7 : 62 : 185 entities Detail

Interaction partners 1. FGF-1, : 9 interactors Detail

More details for 9 interactors identified by 8 citations

Experiments performed 7 experiments Detail

1 NOESY

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

2 1H-15N HSQC

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

3 1H-15N NOESY-HSQC

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

4 1H-15N TOCSY-HSQC

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

5 HNCO

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

6 HNCA

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

7 HN(CO)CA

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian Inova (750 MHz)

Sample #1

Temperature 298 (±0.2) K, pH 6.0 (±0.2), Details 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	acidic fibroblast growth factor	[U-95% 15N]	1 mM
2	heparin like hexasaccharide		1 mM
3	sodium phosphate		10 mM
4	sodium chloride		150 mM
5	3-trimethylsilylpropionate		1 mM

Sample #2

Temperature 298 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
6	acidic fibroblast growth factor	[U-95% 13C; U-95% 15N]	1 mM
7	heparin like hexasaccharide		1 mM
8	sodium phosphate		10 mM
9	sodium chloride		150 mM
10	3-trimethylsilylpropionate		1 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6875_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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:1:IDS:O4	2:2:GNS:C1	unknown	unknown	n/a
2:2:GNS:O4	2:3:IDR:C1	unknown	unknown	n/a
2:3:IDR:O4	2:4:NGY:C1	unknown	unknown	n/a
2:4:NGY:O4	2:5:IDS:C1	unknown	unknown	n/a
2:5:IDS:O4	2:6:GNS:C1	unknown	unknown	n/a
2:6:GNS:O4	2:7:IPA:C2	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr6875_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chemical_shift_1	Warning	1140		95.7 (chain: 1, length: 139)
1	Chemical shift references	chemical_shift_reference	OK	4		No information

Assigned chemical shifts

Saveframe: chemical_shift_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 139, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 780
  - ¹⁵N chemical shifts: 125
  - ¹³C chemical shifts: 235
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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)
23	ARG	HH11	9.73
122	THR	HG1	6.32

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	859	666	77.5
¹⁵N chemical shifts	152	125	82.2
¹³C chemical shifts	633	235	37.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	283	263	92.9
¹⁵N chemical shifts	131	119	90.8
¹³C chemical shifts	278	235	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	576	403	70.0
¹⁵N chemical shifts	21	6	28.6
¹³C chemical shifts	355	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	56	83.6
¹³C chemical shifts	67	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	60	88.2
¹⁵N chemical shifts	1	0	0.0
¹³C chemical shifts	67	0	0.0

Keywords FIBROBLAST GROWTH FACTOR, HEPARIN-LIKE HEXAsaccharide, PROTEIN-CARBOHYDRATE COMPLEX

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Found 1 Document (1.739 seconds)

BMRB: 6875

Sample #1

Sample #2

Related entities 1. FGF-1, : 1 : 15 : 7 : 62 : 185 entities Detail

Interaction partners 1. FGF-1, : 9 interactors Detail

Experiments performed 7 experiments Detail

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Chemical shift validation 4 contents Detail