BMRBj - BMREntryMaster

Found 1 Document (1.213 seconds)

BMRB: 30572

6NZN

Dimer-of-dimer amyloid fibril structure of glucagon

Authors

Hong, M., Gelenter, M.D., Smith, K.J., Liao, S.Y., Mandala, V.S., Dregni, A.J., Lamm, M.S., Tian, Y., Wei, X., Pochan, D.J., Tucker, T.J., Su, Y.

Assembly

Glucagon

Entity

1. Glucagon (polymer, Thiol state: not present), 29 monomers, 3482.747 × 16 Da Detail

HSQGTFTSDY SKYLDSRRAQ DFVQWLMNT

Total weight

55723.953 Da

Max. entity weight

3482.747 Da

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 99.4 %, Completeness (bb): 99.1 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	99.4 % (167 of 168)	99.3 % (133 of 134)	100.0 % (34 of 34)
Backbone	99.1 % (114 of 115)	98.8 % (85 of 86)	100.0 % (29 of 29)
Sidechain	100.0 % (81 of 81)	100.0 % (76 of 76)	100.0 % (5 of 5)
Aromatic	100.0 % (26 of 26)	100.0 % (25 of 25)	100.0 % (1 of 1)
Methyl	100.0 % (10 of 10)	100.0 % (10 of 10)

1. entity 1

HSQGTFTSDY SKYLDSRRAQ DFVQWLMNT

Show sample condition

Sample #1

Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-G4,S8,L14,A19,V23 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
1	Glucagon	{U-13C; U-15N]-G4,S8,L14,A19,V23		0.1 (±0.02) mg/uL

Sample #2

Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

Sample #3

Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
3	Glucagon	{U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24		0.1 (±0.02) mg/uL

Sample #4

Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
4	Glucagon	{U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19		0.1 (±0.02) mg/uL

Protein Blocks Logo

Calculated from 10 models in PDB: 6NZN, Strand ID: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P Detail

Release date

2019-03-26

Citation

The peptide hormone glucagon forms amyloid fibrils with two coexisting β-strand conformations
Gelenter, M.D., Smith, K.J., Liao, S.Y., Mandala, V.S., Dregni, A.J., Lamm, M.S., Tian, Y., Wei, X., Pochan, D.J., Tucker, T.J., Su, Y., Hong, M.
Nat. Struct. Mol. Biol. (2019), 26, 592-598, PubMed 31235909 , DOI 10.1038/s41594-019-0238-6 , Abstract

Related entities 1. Glucagon, : 1 : 26 : 15 : 7 : 172 entities Detail

Interaction partners 1. Glucagon, : 6 interactors Detail

More details for 6 interactors identified by 5 citations

Experiments performed 16 experiments Detail

1 2D 13C-13C CORD

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-G4,S8,L14,A19,V23 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
1	Glucagon	{U-13C; U-15N]-G4,S8,L14,A19,V23		0.1 (±0.02) mg/uL

2 2D 13C-13C CORD

Instrument

Bruker AvanceIII-HD - 600 MHz

Sample

State isotropic, Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

3 2D 15N-13C PERSPIRATION-CP

Instrument

Bruker AvanceIII-HD - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

4 2D 13C-13C PAR

Instrument

Bruker AvanceIII-HD - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

5 2D CHHC

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

6 2D 15N-13C NCCX

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

7 3D 15N-13C-13C NCCX

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
4	Glucagon	{U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19		0.1 (±0.02) mg/uL

8 3D 15N-13C-13C NCACX

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
3	Glucagon	{U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24		0.1 (±0.02) mg/uL

9 3D 15N-13C-13C NCOCX

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Glucagon	{U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24		0.1 (±0.02) mg/uL

10 2D 15N-13C NCA

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system water, Pressure 1 (±0.01) atm, Temperature 293 (±0.2) K, pH 2.0 (±0.1), Details 0.1 mg/uL {U-13C; U-15N]-G4,S8,L14,A19,V23 Glucagon, water

#	Name	Isotope labeling	Type	Concentration
1	Glucagon	{U-13C; U-15N]-G4,S8,L14,A19,V23		0.1 (±0.02) mg/uL

11 2D 13C-13C CORD

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Glucagon	{U-13C; U-15N]-S2,Q3,G4,T5,Q24,W25,L26,M27,N28		0.1 (±0.02) mg/uL

12 2D CHHC

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
4	Glucagon	{U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19		0.1 (±0.02) mg/uL

13 2D 13C-13C CORD

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
4	Glucagon	{U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19		0.1 (±0.02) mg/uL

14 2D-13C-13C CORD

Instrument

Bruker AvanceIII-HD - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
4	Glucagon	{U-13C; U-15N]-S11,K12,Y13,L14,D15,S16,R17,R18,A19		0.1 (±0.02) mg/uL

15 2D 13C-13C CORD

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Glucagon	{U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24		0.1 (±0.02) mg/uL

16 2D 13C-13C PDSD

Instrument

Bruker AvanceIII-HD - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Glucagon	{U-13C; U-15N]-T5,F6,T7,S8,D9,Y10,S11,A19,Q20,D21,F22,V23,Q24		0.1 (±0.02) mg/uL

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30572_6nzn.nef
Input source #2: Coordindates	6nzn.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): E vs Auth_asym_ID (model): E

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): F vs Auth_asym_ID (model): F

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): G vs Auth_asym_ID (model): G

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): H vs Auth_asym_ID (model): H

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): I vs Auth_asym_ID (model): I

-------110-------120---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
--------10--------20---------

Entity_assembly_ID (NMR): J vs Auth_asym_ID (model): J

-------110-------120---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
--------10--------20---------

Entity_assembly_ID (NMR): K vs Auth_asym_ID (model): K

-------110-------120---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
--------10--------20---------

Entity_assembly_ID (NMR): L vs Auth_asym_ID (model): L

-------110-------120---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
--------10--------20---------

Entity_assembly_ID (NMR): M vs Auth_asym_ID (model): M

-------110-------120---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
--------10--------20---------

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	29	100.0
B	B	29	100.0
C	C	29	100.0
D	D	29	100.0
E	E	29	100.0
F	F	29	100.0
G	G	29	100.0
H	H	29	100.0
I	I	29	100.0
J	J	29	100.0
K	K	29	100.0
L	L	29	100.0
M	M	29	100.0
A	A	29	100.0
A	A	29	100.0
A	A	29	100.0

Content subtype: combined_30572_6nzn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	392		100.0 (chain: A, length: 29), 100.0 (chain: P, length: 29)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	589 (1)	noe	100.0 (chain: A, length: 29), 100.0 (chain: I, length: 29)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 100.0%

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Entity_assembly_ID: P, Chain length: 29, Sequence coverage: 100.0%

--------10--------20---------
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
|||||||||||||||||||||||||||||
HSQGTFTSDYSKYLDSRRAQDFVQWLMNT

Total number of assignments
- ¹³C chemical shifts: 306
- ¹⁵N chemical shifts: 86

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	HIS	CG	127.6
1	HIS	ND1	180.4
1	HIS	NE2	174.1
3	GLN	CD	179.2
6	PHE	CG	136.6
9	ASP	CG	174.4
10	TYR	CG	129.5
10	TYR	CZ	154.8
12	LYS	NZ	33.7
13	TYR	CG	128.4
13	TYR	CZ	155.5
15	ASP	CG	175.4
17	ARG	CZ	158.3
17	ARG	NH1	72.5
17	ARG	NH2	72.5
18	ARG	CZ	158.3
18	ARG	NH1	72.5
18	ARG	NH2	72.5
20	GLN	CD	178.9
21	ASP	CG	174.2
22	PHE	CG	137.1
24	GLN	CD	178.4
25	TRP	CD2	130.6
25	TRP	CE2	136.0
25	TRP	CG	109.2
28	ASN	CG	175.1

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	134	134	100.0
¹⁵N chemical shifts	36	36	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	58	58	100.0
¹⁵N chemical shifts	29	29	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	76	76	100.0
¹⁵N chemical shifts	7	7	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	11	11	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	25	25	100.0
¹⁵N chemical shifts	1	1	100.0

Entity_assemble_ID: P

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	HIS	CG	126.9
1	HIS	ND1	179.9
1	HIS	NE2	174.1
3	GLN	CD	178.7
6	PHE	CG	135.8
9	ASP	CG	174.4
10	TYR	CG	129.5
10	TYR	CZ	154.8
12	LYS	NZ	33.7
13	TYR	CG	128.4
13	TYR	CZ	155.5
15	ASP	CG	175.4
17	ARG	CZ	158.3
17	ARG	NH1	72.5
17	ARG	NH2	72.5
18	ARG	CZ	158.3
18	ARG	NH1	72.5
18	ARG	NH2	72.5
20	GLN	CD	178.9
21	ASP	CG	174.2
22	PHE	CG	136.5
24	GLN	CD	179.5
25	TRP	CD2	130.6
25	TRP	CE2	136.0
25	TRP	CG	109.2
28	ASN	CG	174.7

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	134	134	100.0
¹⁵N chemical shifts	36	36	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	58	58	100.0
¹⁵N chemical shifts	29	29	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	76	76	100.0
¹⁵N chemical shifts	7	7	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	11	11	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	25	25	100.0
¹⁵N chemical shifts	1	1	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: A
- Chain_ID: P

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 100.0%
  - Entity_assembly_ID: I, Chain length: 29, Sequence coverage: 100.0%
- Total number of restraints: 589
- Weight of restraints: 1.0 (589)
- Potential type of restraints: upper-bound-parabolic (589)
- Range of distance target values: 0.0, 10.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
  - Chain_ID: D
    None
  - Chain_ID: E
    None
  - Chain_ID: F
    None
  - Chain_ID: G
    None
  - Chain_ID: H
    None
  - Chain_ID: I
  - Chain_ID: J
    None
  - Chain_ID: K
    None
  - Chain_ID: L
    None
  - Chain_ID: M
    None
  - Chain_ID: N
    None
  - Chain_ID: O
    None
  - Chain_ID: P
    None
- Distance restraints on contact map

Keywords amyloid, hormone

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Found 1 Document (1.213 seconds)

BMRB: 30572

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Glucagon, : 1 : 26 : 15 : 7 : 172 entities Detail

Interaction partners 1. Glucagon, : 6 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 3 contents Detail